1
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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2
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Neumann JS, Desalle R, Narechania A, Schierwater B, Tessler M. Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets. Syst Biol 2021; 70:360-375. [PMID: 32462193 PMCID: PMC7875439 DOI: 10.1093/sysbio/syaa038] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/27/2020] [Accepted: 01/29/2020] [Indexed: 12/19/2022] Open
Abstract
There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets ($\sim $45,000-400,000 characters in size with $\sim $15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets ($\sim $15-275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10$\times $ in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets ($>$200,000 characters and up to $\sim $100 taxa) showing node stability even with $\geqq100\times $ upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.].
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Affiliation(s)
- Johannes S Neumann
- Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Rob Desalle
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Bernd Schierwater
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
- ITZ, Division of Ecology and Evolution, Tierärztliche Hochschule Hannover, Bünteweg 9, 30559 Hannover, Germany
| | - Michael Tessler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
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3
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits. Sci Rep 2019; 9:17561. [PMID: 31772223 PMCID: PMC6879607 DOI: 10.1038/s41598-019-54037-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain "Panama"). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, Institute of Animal Ecology, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA.
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4
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Abstract
Schierwater & DeSalle introduce the enigmatic phylum Placozoa.
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Affiliation(s)
- Bernd Schierwater
- TiHo Hannover, ITZ Ecology & Evolution, Buenteweg 17d, 30559 Hannover.
| | - Rob DeSalle
- Comparative Genomics Institute at the American Museum of Natural History, 79th Street at Central Park West, New York, NY 10024, USA
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5
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Hoffmeier A, Gramzow L, Bhide AS, Kottenhagen N, Greifenstein A, Schubert O, Mummenhoff K, Becker A, Theißen G. A Dead Gene Walking: Convergent Degeneration of a Clade of MADS-Box Genes in Crucifers. Mol Biol Evol 2019; 35:2618-2638. [PMID: 30053121 DOI: 10.1093/molbev/msy142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Genes are "born," and eventually they "die." These processes shape the phenotypic evolution of organisms and are hence of great biological interest. If genes die in plants, they generally do so quite rapidly. Here, we describe the fate of GOA-like genes that evolve in a dramatically different manner. GOA-like genes belong to the subfamily of Bsister genes of MIKC-type MADS-box genes. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS-like genes, a clade of Bsister genes, are indeed highly conserved in crucifers (Brassicaceae) maintaining the ancestral function of Bsister genes in ovule and seed development. In contrast, their closest paralogs, the GOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA-like genes occurred after millions of years of coexistence with ABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration, a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. Delayed Convergent Asymmetric Degeneration of GOA-like genes may have been initiated by a reduction in the expression of an ancestral GOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
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Affiliation(s)
- Andrea Hoffmeier
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Lydia Gramzow
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Amey S Bhide
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Nina Kottenhagen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Andreas Greifenstein
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
| | - Olesia Schubert
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Becker
- Plant Developmental Biology Group, Institute of Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Günter Theißen
- Genetics, Matthias Schleiden Institute, Friedrich-Schiller-University Jena, Jena, Germany
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6
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Albertini MC, Fraternale D, Semprucci F, Cecchini S, Colomba M, Rocchi MBL, Sisti D, Di Giacomo B, Mari M, Sabatini L, Cesaroni L, Balsamo M, Guidi L. Bioeffects of Prunus spinosa L. fruit ethanol extract on reproduction and phenotypic plasticity of Trichoplax adhaerens Schulze, 1883 (Placozoa). PeerJ 2019; 7:e6789. [PMID: 31024778 PMCID: PMC6475577 DOI: 10.7717/peerj.6789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/14/2019] [Indexed: 12/17/2022] Open
Abstract
The aim of this work was to test and analyse the bioeffects of Prunus spinosa L. (Rosacaee) fruit ethanol extract on Trichoplax adhaerens Schulze, 1883 (Placozoa) laboratory cultures which—for the first time—were employed as in vivo biological model to assess the bioactivity of a natural extract. The ethanol extract of P. spinosa was administrated during a 46 day experimental period; ultrastructural (by optical, confocal, TEM and SEM microscopy) and morphometric analyses indicated that treated Trichoplax adhaerens showed significant differences in viability, reproductive modalities, body shape and colour with respect to the control group. Finally, P. spinosa bioactive compounds seem to exert profound protective effects on T. adhaerens reproduction and phenotype. Our results may support additional investigations related to other bioactive compounds properties useful for nutraceutical preparations to be used as food supplements.
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Affiliation(s)
| | - Daniele Fraternale
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Federica Semprucci
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Silvio Cecchini
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Mariastella Colomba
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Marco B L Rocchi
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Davide Sisti
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Barbara Di Giacomo
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Michele Mari
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Luigia Sabatini
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Lucia Cesaroni
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Maria Balsamo
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
| | - Loretta Guidi
- Department of Biomolecular Sciences, University of Urbino, Urbino, Pesaro-Urbino, Italia
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7
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Kamm K, Schierwater B, DeSalle R. Innate immunity in the simplest animals - placozoans. BMC Genomics 2019; 20:5. [PMID: 30611207 PMCID: PMC6321704 DOI: 10.1186/s12864-018-5377-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/16/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling. RESULTS A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa. CONCLUSIONS The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.
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Affiliation(s)
- Kai Kamm
- ITZ Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17d, D-30559 Hannover, Germany
| | - Bernd Schierwater
- ITZ Ecology and Evolution, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17d, D-30559 Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
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8
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Gul IS, Staal J, Hulpiau P, De Keuckelaere E, Kamm K, Deroo T, Sanders E, Staes K, Driege Y, Saeys Y, Beyaert R, Technau U, Schierwater B, van Roy F. GC Content of Early Metazoan Genes and Its Impact on Gene Expression Levels in Mammalian Cell Lines. Genome Biol Evol 2018; 10:909-917. [PMID: 29608715 PMCID: PMC5952964 DOI: 10.1093/gbe/evy040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
With the genomes available for many animal clades, including the early-branching metazoans, one can readily study the functional conservation of genes across a diversity of animal lineages. Ectopic expression of an animal protein in, for instance, a mammalian cell line is a generally used strategy in structure–function analysis. However, this might turn out to be problematic in case of distantly related species. Here we analyzed the GC content of the coding sequences of basal animals and show its impact on gene expression levels in human cell lines, and, importantly, how this expression efficiency can be improved. Optimization of the GC3 content in the coding sequences of cadherin, alpha-catenin, and paracaspase of Trichoplax adhaerens dramatically increased the expression of these basal animal genes in human cell lines.
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Affiliation(s)
- Ismail Sahin Gul
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Jens Staal
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Paco Hulpiau
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Evi De Keuckelaere
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Kai Kamm
- Institut für Tierökologie und Zellbiologie (ITZ), Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
| | - Tom Deroo
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Ellen Sanders
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Katrien Staes
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Yasmine Driege
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Yvan Saeys
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Ulrich Technau
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Austria
| | - Bernd Schierwater
- Institut für Tierökologie und Zellbiologie (ITZ), Division of Ecology and Evolution, Stiftung Tieraerztliche Hochschule Hannover, Hannover, Germany
| | - Frans van Roy
- Center for Inflammation Research, Flanders Institute for Biotechnology (VIB), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Belgium
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9
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Abstract
The origin of animals, one of the major transitions in evolution, remains mysterious. Many key aspects of animal evolution can be reconstructed by comparing living species within a robust phylogenetic framework. However, uncertainty remains regarding the evolutionary relationships between two ancient animal lineages - sponges and ctenophores - and the remaining animal phyla. Comparative morphology and some phylogenomic analyses support the view that sponges represent the sister lineage to the rest of the animals, while other phylogenomic analyses support ctenophores, a phylum of carnivorous, gelatinous marine organisms, as the sister lineage. Here, we explore why different studies yield different answers and discuss the implications of the two alternative hypotheses for understanding the origin of animals. Reconstruction of ancient evolutionary radiations is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits. Rather than staking out positions in favor of the ctenophores-sister or the sponges-sister hypothesis, we submit that research programs aimed at understanding the biology of the first animals should instead embrace the uncertainty surrounding early animal evolution in their experimental designs.
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10
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Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B. Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction. Sci Rep 2018; 8:11168. [PMID: 30042472 PMCID: PMC6057997 DOI: 10.1038/s41598-018-29400-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/09/2018] [Indexed: 12/24/2022] Open
Abstract
The phylum Placozoa officially consists of only a single described species, Trichoplax adhaerens, although several lineages can be separated by molecular markers, geographical distributions and environmental demands. The placozoan 16S haplotype H2 (Trichoplax sp. H2) is the most robust and cosmopolitan lineage of placozoans found to date. In this study, its genome was found to be distinct but highly related to the Trichoplax adhaerens reference genome, for remarkably unique reasons. The pattern of variation and allele distribution between the two lineages suggests that both originate from a single interbreeding event in the wild, dating back at least several decades ago, and both seem not to have engaged in sexual reproduction since. We conclude that populations of certain placozoan haplotypes remain stable for long periods without bisexual reproduction. Furthermore, allelic variation within and between the two Trichoplax lineages indicates that successful bisexual reproduction between related placozoan lineages might serve to either counter accumulated negative somatic mutations or to cope with changing environmental conditions. On the other hand, enrichment of neutral or beneficial somatic mutations by vegetative reproduction, combined with rare sexual reproduction, could instantaneously boost genetic variation, generating novel ecotypes and eventually species.
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Affiliation(s)
- Kai Kamm
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany.
| | - Hans-Jürgen Osigus
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Bernd Schierwater
- University of Veterinary Medicine Hannover, Foundation, ITZ Ecology and Evolution, Bünteweg 17d, D-30559, Hannover, Germany. .,Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA. .,Yale University, Molecular, Cellular and Developmental Biology, New Haven, CT, 06520, USA.
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11
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Novotný JP, Chughtai AA, Kostrouchová M, Kostrouchová V, Kostrouch D, Kaššák F, Kaňa R, Schierwater B, Kostrouchová M, Kostrouch Z. Trichoplax adhaerens reveals a network of nuclear receptors sensitive to 9- cis-retinoic acid at the base of metazoan evolution. PeerJ 2017; 5:e3789. [PMID: 28975052 PMCID: PMC5624297 DOI: 10.7717/peerj.3789] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022] Open
Abstract
Trichoplax adhaerens, the only known species of Placozoa is likely to be closely related to an early metazoan that preceded branching of Cnidaria and Bilateria. This animal species is surprisingly well adapted to free life in the World Ocean inhabiting tidal costal zones of oceans and seas with warm to moderate temperatures and shallow waters. The genome of T. adhaerens (sp. Grell) includes four nuclear receptors, namely orthologue of RXR (NR2B), HNF4 (NR2A), COUP-TF (NR2F) and ERR (NR3B) that show a high degree of similarity with human orthologues. In the case of RXR, the sequence identity to human RXR alpha reaches 81% in the DNA binding domain and 70% in the ligand binding domain. We show that T. adhaerens RXR (TaRXR) binds 9-cis retinoic acid (9-cis-RA) with high affinity, as well as high specificity and that exposure of T. adhaerens to 9-cis-RA regulates the expression of the putative T. adhaerens orthologue of vertebrate L-malate-NADP+ oxidoreductase (EC 1.1.1.40) which in vertebrates is regulated by a heterodimer of RXR and thyroid hormone receptor. Treatment by 9-cis-RA alters the relative expression profile of T. adhaerens nuclear receptors, suggesting the existence of natural ligands. Keeping with this, algal food composition has a profound effect on T. adhaerens growth and appearance. We show that nanomolar concentrations of 9-cis-RA interfere with T. adhaerens growth response to specific algal food and causes growth arrest. Our results uncover an endocrine-like network of nuclear receptors sensitive to 9-cis-RA in T. adhaerens and support the existence of a ligand-sensitive network of nuclear receptors at the base of metazoan evolution.
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Affiliation(s)
- Jan Philipp Novotný
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Medicine V., University of Heidelberg, Heidelberg, Germany
| | - Ahmed Ali Chughtai
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Markéta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic.,Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - David Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Filip Kaššák
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Radek Kaňa
- Institute of Microbiology, Laboratory of Photosynthesis, Czech Academy of Sciences, Třeboň, Czech Republic
| | - Bernd Schierwater
- Institute for Animal Ecology and Cell Biology, University of Veterinary Medicine, Hannover, Germany.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States of America
| | - Marta Kostrouchová
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Zdenek Kostrouch
- Biocev, First Faculty of Medicine, Charles University, Vestec, Czech Republic
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Schleicherová D, Dulias K, Osigus HJ, Paknia O, Hadrys H, Schierwater B. The most primitive metazoan animals, the placozoans, show high sensitivity to increasing ocean temperatures and acidities. Ecol Evol 2017; 7:895-904. [PMID: 28168026 PMCID: PMC5288258 DOI: 10.1002/ece3.2678] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 11/09/2016] [Accepted: 11/13/2016] [Indexed: 01/14/2023] Open
Abstract
The increase in atmospheric carbon dioxide (CO2) leads to rising temperatures and acidification in the oceans, which directly or indirectly affects all marine organisms, from bacteria to animals. We here ask whether the simplest-and possibly also the oldest-metazoan animals, the placozoans, are particularly sensitive to ocean warming and acidification. Placozoans are found in all warm and temperate oceans and are soft-bodied, microscopic invertebrates lacking any calcified structures, organs, or symmetry. We here show that placozoans respond highly sensitive to temperature and acidity stress. The data reveal differential responses in different placozoan lineages and encourage efforts to develop placozoans as a potential biomarker system.
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Affiliation(s)
| | - Katharina Dulias
- ITZ, Ecology and EvolutionTiHo Hannover Hannover Germany; Present address: Department of Biological Sciences School of Applied Sciences University of Huddersfield Huddersfield UK
| | | | - Omid Paknia
- ITZ, Ecology and Evolution TiHo Hannover Hannover Germany
| | - Heike Hadrys
- ITZ, Ecology and Evolution TiHo Hannover Hannover Germany
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New Insights Into the Roles of Retinoic Acid Signaling in Nervous System Development and the Establishment of Neurotransmitter Systems. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 330:1-84. [PMID: 28215529 DOI: 10.1016/bs.ircmb.2016.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Secreted chiefly from the underlying mesoderm, the morphogen retinoic acid (RA) is well known to contribute to the specification, patterning, and differentiation of neural progenitors in the developing vertebrate nervous system. Furthermore, RA influences the subtype identity and neurotransmitter phenotype of subsets of maturing neurons, although relatively little is known about how these functions are mediated. This review provides a comprehensive overview of the roles played by RA signaling during the formation of the central and peripheral nervous systems of vertebrates and highlights its effects on the differentiation of several neurotransmitter systems. In addition, the evolutionary history of the RA signaling system is discussed, revealing both conserved properties and alternate modes of RA action. It is proposed that comparative approaches should be employed systematically to expand our knowledge of the context-dependent cellular mechanisms controlled by the multifunctional signaling molecule RA.
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