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Eitel M, Osigus H, Brenzinger B, Wörheide G. Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics. Ecol Evol 2024; 14:e11220. [PMID: 38606341 PMCID: PMC11007570 DOI: 10.1002/ece3.11220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.
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Affiliation(s)
- Michael Eitel
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
| | - Hans‐Jürgen Osigus
- Institut für TierökologieStiftung Tierärztliche Hochschule HannoverHannoverDeutschland
- Present address:
Hochschulbibliothek, Stiftung Tierärztliche Hochschule HannoverHannoverDeutschland
| | - Bastian Brenzinger
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Zoologische StaatssammlungMünchenDeutschland
| | - Gert Wörheide
- GeoBio‐CenterLudwig‐Maximilians‐Universität MünchenMünchenDeutschland
- Department of Earth and Environmental Sciences, Paleontology and GeobiologyLudwig‐Maximilians‐Universität‐MünchenMünchenDeutschland
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB) – Bayerische Staatssammlung für Paläontologie und GeologieMünchenDeutschland
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2
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Romanova DY, Varoqueaux F, Eitel M, Yoshida MA, Nikitin MA, Moroz LL. Long-Term Culturing of Placozoans (Trichoplax and Hoilungia). Methods Mol Biol 2024; 2757:509-529. [PMID: 38668981 DOI: 10.1007/978-1-0716-3642-8_21] [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] [Indexed: 05/01/2024]
Abstract
The phylum Placozoa remains one of the least explored among early-branching metazoan lineages. For over 130 years, this phylum had been represented by the single species Trichoplax adhaerens-an animal with the simplest known body plan (three cell layers without any organs) but complex behaviors. Recently, extensive sampling of placozoans across the globe and their subsequent genetic analysis have revealed incredible biodiversity with numerous cryptic species worldwide. However, only a few culture protocols are available to date, and all are for one species only. Here, we describe the breeding of four different species representing two placozoan genera: Trichoplax adhaerens, Trichoplax sp. H2, Hoilungia sp. H4, and Hoilungia hongkongensis originating from diverse biotopes. Our protocols allow to culture all species under comparable conditions. Next, we outlined various food sources and optimized strain-specific parameters enabling long-term culturing. These protocols can facilitate comparative analyses of placozoan biology and behaviors, which together will contribute to deciphering general principles of animal organization.
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Affiliation(s)
- Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia.
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.
| | - Michael Eitel
- Department of Earth and Environmental Sciences Palaeontology & Geobiology, LMU München, Munich, Germany
| | - Masa-Aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Oki, Shimane, Japan
| | - Mikhail A Nikitin
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Leonid L Moroz
- Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
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3
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Romanova DY, Moroz LL. Brief History of Placozoa. Methods Mol Biol 2024; 2757:103-122. [PMID: 38668963 DOI: 10.1007/978-1-0716-3642-8_3] [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] [Indexed: 05/04/2024]
Abstract
Placozoans are morphologically the simplest free-living animals. They represent a unique window of opportunities to understand both the origin of the animal organization and the rules of life for the system and synthetic biology of the future. However, despite more than 100 years of their investigations, we know little about their organization, natural habitats, and life strategies. Here, we introduce this unique animal phylum and highlight some directions vital to broadening the frontiers of the biomedical sciences. In particular, understanding the genomic bases of placozoan biodiversity, cell identity, connectivity, reproduction, and cellular bases of behavior are critical hot spots for future studies.
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Affiliation(s)
- Daria Y Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russian Federation.
| | - Leonid L Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
- Whitney Laboratory for Marine Biosciences University of Florida, St. Augustine, FL, USA.
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4
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Haas E, Kim Y, Stanley D. Why can insects not biosynthesize cholesterol? ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 112:e21983. [PMID: 36372906 DOI: 10.1002/arch.21983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Two aspects of insect lipid biochemistry differ from the mammalian background. In one aspect, nearly a hundred years ago scientists demonstrated that the polyunsaturated fatty acid (PUFAs), linoleic acid (LA; 18:2n-6) is an essential nutrient in the diets of all mammals that have been studied in that regard. An unknown number of insect species are able to biosynthesize LA de novo. Some species take the biosynthesized LA into fatty acid elongation/desaturation pathways to produce other PUFAs, 18:3n-6, 20:3n-6 and 20:4n-6. A couple of species use the de novo produced LA to biosynthesize prostaglandins and other eicosanoids, short-lived signal moieties that mediate important physiological actions in immunity and reproduction. Insects differ from mammals, also, in their lack of genes that encode enzymes acting in biosynthesis of cholesterol. Insects require dietary cholesterol to meet their cellular, physiological, developmental, and reproductive needs. Looking at a broader view of invertebrate biochemistry, most protostomes lost all or most genes involved in cholesterol biosynthesis. The massive gene loss occurred during the Ediacaran Period, which lasted 96 million years, from the end of the Cryogenian Period (635 million years ago; MYA) to the beginning of the Cambrian Period (538.6 MYA). The key point here is that the inability to biosynthesize cholesterol is not limited to insects; it occured in most protostomes. We address the protostome need and benefits of acquiring exogenous sterols.
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Affiliation(s)
- Eric Haas
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska, USA
| | - Yonggyun Kim
- Department of Plant Medicals, College of Life Sciences, Andong National University, Andong, Republic of Korea
| | - David Stanley
- Biological Control of Insect Research Laboratory, USDA-Agricultural Research Service, Columbia, Missouri, USA
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5
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Tessler M, Neumann JS, Kamm K, Osigus HJ, Eshel G, Narechania A, Burns JA, DeSalle R, Schierwater B. Phylogenomics and the first higher taxonomy of Placozoa, an ancient and enigmatic animal phylum. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1016357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Placozoa is an ancient phylum of extraordinarily unusual animals: miniscule, ameboid creatures that lack most fundamental animal features. Despite high genetic diversity, only recently have the second and third species been named. While prior genomic studies suffer from incomplete placozoan taxon sampling, we more than double the count with protein sequences from seven key genomes and produce the first nuclear phylogenomic reconstruction of all major placozoan lineages. This leads us to the first complete Linnaean taxonomic classification of Placozoa, over a century after its discovery: This may be the only time in the 21st century when an entire higher taxonomy for a whole animal phylum is formalized. Our classification establishes 2 new classes, 4 new orders, 3 new families, 1 new genus, and 1 new species, namely classes Polyplacotomia and Uniplacotomia; orders Polyplacotomea, Trichoplacea, Cladhexea, and Hoilungea; families Polyplacotomidae, Cladtertiidae, and Hoilungidae; and genus Cladtertia with species Cladtertia collaboinventa, nov. Our likelihood and gene content tree topologies refine the relationships determined in previous studies. Adding morphological data into our phylogenomic matrices suggests sponges (Porifera) as the sister to other animals, indicating that modest data addition shifts this node away from comb jellies (Ctenophora). Furthermore, by adding the first genomic protein data of the exceptionally distinct and branching Polyplacotoma mediterranea, we solidify its position as sister to all other placozoans; a divergence we estimate to be over 400 million years old. Yet even this deep split sits on a long branch to other animals, suggesting a bottleneck event followed by diversification. Ancestral state reconstructions indicate large shifts in gene content within Placozoa, with Hoilungia hongkongensis and its closest relatives having the most unique genetics.
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6
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Romanova DY, Nikitin MA, Shchenkov SV, Moroz LL. Expanding of Life Strategies in Placozoa: Insights From Long-Term Culturing of Trichoplax and Hoilungia. Front Cell Dev Biol 2022; 10:823283. [PMID: 35223848 PMCID: PMC8864292 DOI: 10.3389/fcell.2022.823283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/20/2022] [Indexed: 12/05/2022] Open
Abstract
Placozoans are essential reference species for understanding the origins and evolution of animal organization. However, little is known about their life strategies in natural habitats. Here, by maintaining long-term culturing for four species of Trichoplax and Hoilungia, we extend our knowledge about feeding and reproductive adaptations relevant to the diversity of life forms and immune mechanisms. Three modes of population dynamics depended upon feeding sources, including induction of social behaviors, morphogenesis, and reproductive strategies. In addition to fission, representatives of all species produced “swarmers” (a separate vegetative reproduction stage), which could also be formed from the lower epithelium with greater cell-type diversity. We monitored the formation of specialized spheroid structures from the upper cell layer in aging culture. These “spheres” could be transformed into juvenile animals under favorable conditions. We hypothesize that spheroid structures represent a component of the innate immune defense response with the involvement of fiber cells. Finally, we showed that regeneration could be a part of the adaptive reproductive strategies in placozoans and a unique experimental model for regenerative biology.
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Affiliation(s)
- Daria Y. Romanova
- Institute of Higher Nervous Activity and Neurophysiology of RAS, Moscow, Russia
- *Correspondence: Daria Y. Romanova, ; Leonid L. Moroz,
| | - Mikhail A. Nikitin
- Belozersky Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Sergey V. Shchenkov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Leonid L. Moroz
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, United States
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, United States
- *Correspondence: Daria Y. Romanova, ; Leonid L. Moroz,
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7
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Kawashima T, Yoshida MA, Miyazawa H, Nakano H, Nakano N, Sakamoto T, Hamada M. Observing Phylum-Level Metazoan Diversity by Environmental DNA Analysis at the Ushimado Area in the Seto Inland Sea. Zoolog Sci 2022; 39:157-165. [DOI: 10.2108/zs210073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Takeshi Kawashima
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center Biological Resources, Faculty of Life and Environmental Science, Shimane University, Shimane 685-0024, Japan
| | - Hideyuki Miyazawa
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka 415-0025, Japan
| | - Natumi Nakano
- Department of Biology, Nara Medical University, Nara 634-8521, Japan
| | - Tatsuya Sakamoto
- Ushimado Marine Institute, Okayama University, Okayama 701-4303, Japan
| | - Mayuko Hamada
- Ushimado Marine Institute, Okayama University, Okayama 701-4303, Japan
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8
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Schierwater B, Osigus HJ, Bergmann T, Blackstone NW, Hadrys H, Hauslage J, Humbert PO, Kamm K, Kvansakul M, Wysocki K, DeSalle R. The enigmatic Placozoa part 1: Exploring evolutionary controversies and poor ecological knowledge. Bioessays 2021; 43:e2100080. [PMID: 34472126 DOI: 10.1002/bies.202100080] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E. Schulze in 1883, it attracted attention as a potential model for the ancestral state of metazoan organization, the "Urmetazoon". Trichoplax lacks any kind of symmetry, organs, nerve cells, muscle cells, basal lamina, and extracellular matrix. Furthermore, the placozoan genome is the smallest (not secondarily reduced) genome of all metazoan genomes. It harbors a remarkably rich diversity of genes and has been considered the best living surrogate for a metazoan ancestor genome. The phylum Placozoa presently harbors three formally described species, while several dozen "cryptic" species are yet awaiting their description. The phylogenetic position of placozoans has recently become a contested arena for modern phylogenetic analyses and view-driven claims. Trichoplax offers unique prospects for understanding the minimal requirements of metazoan animal organization and their corresponding malfunctions.
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Affiliation(s)
- Bernd Schierwater
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Tjard Bergmann
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Neil W Blackstone
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Heike Hadrys
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jens Hauslage
- Gravitational Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Patrick O Humbert
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kai Kamm
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Kathrin Wysocki
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rob DeSalle
- American Museum of Natural History, New York, New York, USA
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9
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Romanova DY, Varoqueaux F, Daraspe J, Nikitin MA, Eitel M, Fasshauer D, Moroz LL. Hidden cell diversity in Placozoa: ultrastructural insights from Hoilungia hongkongensis. Cell Tissue Res 2021; 385:623-637. [PMID: 33876313 PMCID: PMC8523601 DOI: 10.1007/s00441-021-03459-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/31/2021] [Indexed: 12/17/2022]
Abstract
From a morphological point of view, placozoans are among the most simple free-living animals. This enigmatic phylum is critical for our understanding of the evolution of animals and their cell types. Their millimeter-sized, disc-like bodies consist of only three cell layers that are shaped by roughly seven major cell types. Placozoans lack muscle cells and neurons but are able to move using their ciliated lower surface and take up food in a highly coordinated manner. Intriguingly, the genome of Trichoplax adhaerens, the founding member of the enigmatic phylum, has disclosed a surprising level of genetic complexity. Moreover, recent molecular and functional investigations have uncovered a much larger, so-far hidden cell-type diversity. Here, we have extended the microanatomical characterization of a recently described placozoan species-Hoilungia hongkongensis. In H. hongkongensis, we recognized the established canonical three-layered placozoan body plan but also came across several morphologically distinct and potentially novel cell types, among them novel gland cells and "shiny spheres"-bearing cells at the upper epithelium. Thus, the diversity of cell types in placozoans is indeed higher than anticipated.
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Affiliation(s)
- Daria Y Romanova
- Department of Fundamental Neurosciences, University of Lausanne, 1005, Lausanne, Switzerland.
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Moscow, 117485, Russia.
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, 1005, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Mikhail A Nikitin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119991, Russia
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians Universität München, Munich, Germany
| | - Dirk Fasshauer
- Department of Fundamental Neurosciences, University of Lausanne, 1005, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Leonid L Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, 32080, USA.
- Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
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10
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Beljan S, Herak Bosnar M, Ćetković H. Rho Family of Ras-Like GTPases in Early-Branching Animals. Cells 2020; 9:cells9102279. [PMID: 33066017 PMCID: PMC7600811 DOI: 10.3390/cells9102279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Non-bilaterian animals consist of four phyla; Porifera, Cnidaria, Ctenophora, and Placozoa. These early-diverging animals are crucial for understanding the evolution of the entire animal lineage. The Rho family of proteins make up a major branch of the Ras superfamily of small GTPases, which function as key molecular switches that play important roles in converting and amplifying external signals into cellular responses. This review represents a compilation of the current knowledge on Rho-family GTPases in non-bilaterian animals, the available experimental data about their biochemical characteristics and functions, as well as original bioinformatics analysis, in order to gain a general insight into the evolutionary history of Rho-family GTPases in simple animals.
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Affiliation(s)
- Silvestar Beljan
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Division of Molecular Biology, Faculty of Science, University of Zagreb, HR-10000 Zagreb, Croatia
| | - Maja Herak Bosnar
- Division of Molecular Medicine, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, HR-10000 Zagreb, Croatia;
- Correspondence: ; Tel.: +385-1-456-1115
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11
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Miyazawa H, Osigus HJ, Rolfes S, Kamm K, Schierwater B, Nakano H. Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions. Genome Biol Evol 2020; 13:5919586. [PMID: 33031489 PMCID: PMC7813641 DOI: 10.1093/gbe/evaa213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2020] [Indexed: 12/16/2022] Open
Abstract
Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32–43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon–intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.
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Affiliation(s)
- Hideyuki Miyazawa
- Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, Japan.,Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
| | - Hans-Jürgen Osigus
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Sarah Rolfes
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Kai Kamm
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Bernd Schierwater
- Division of Molecular Evolution, Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Germany
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, Japan
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12
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Binary fission in Trichoplax is orthogonal to the subsequent division plane. Mech Dev 2020; 162:103608. [PMID: 32387588 DOI: 10.1016/j.mod.2020.103608] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/09/2020] [Indexed: 11/20/2022]
Abstract
Asexual reproduction in Trichoplax occurs mainly by binary fission and occasionally by the budding of epithelial spheres called "swarmers". The process that leads to binary fission and the mechanisms involved in this segregation are practically unknown. Trichoplax lacks a defined shape, presenting a constantly changing outline due to its continuous movements and body contractions. For this reason, and due to the absence of anatomical references, it has been classified as an asymmetric organism. Here, we report that a transient wound is formed in the marginal epithelium of the two new individuals produced by binary fission. By tracking the location of this epithelial wound, we can determine that successive dichotomous divisions are orthogonal to the previous division. We also found that LiCl paralyzes the cilia beating movement and body contractions and causes the placozoans to become circular in shape. This effect, as well as a stereotypic body folding behavior observed in detached placozoans and cell labeling experiments of the upper epithelium, indicate a cylindrical body symmetry for Placozoa.
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13
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Osigus HJ, Rolfes S, Herzog R, Kamm K, Schierwater B. Polyplacotoma mediterranea is a new ramified placozoan species. Curr Biol 2020; 29:R148-R149. [PMID: 30836080 DOI: 10.1016/j.cub.2019.01.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The enigmatic phylum Placozoa is harboring an unknown number of cryptic species and has become a challenge for modern systematics. Only recently, a second species has been described [1], while the presence of more than a hundred additional species has been suggested [2]. The original placozoan species Trichoplax adhaerens[3], the second species Hoilungia hongkongensis[1] and all yet undescribed species are morphologically indistinguishable (i.e. no species diagnostic characters are available [4]). Here, we report on a new placozoan species, Polyplacotoma mediterranea gen. nov., spec. nov., which differs from other placozoans in its completely different morphological habitus, including long polytomous body branches and a maximum body length of more than 10 mm. Polyplacotoma mediterranea also necessitates a different view of placozoan mitochondrial genetics. P. mediterranea harbors a highly compact mitochondrial genome with overlapping mitochondrial tRNA and protein coding genes. Furthermore, the new species lacks typical placozoan features, including the cox1 micro exon and cox1 barcode intron. As phylogenetic analyses suggest a sister group relationship of P. mediterranea to all other placozoans, this new species may also be relevant for studies addressing the relationships at the base of the metazoan tree of life.
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Affiliation(s)
- Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany.
| | - Sarah Rolfes
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Rebecca Herzog
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Kai Kamm
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology & Evolution, Bünteweg 17d, 30559 Hannover, Germany; American Museum of Natural History, Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, New York, NY, USA; Yale University, Department of Ecology & Evolutionary Biology, New Haven, CT, USA.
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14
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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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15
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Steinmetz PRH. A non-bilaterian perspective on the development and evolution of animal digestive systems. Cell Tissue Res 2019; 377:321-339. [PMID: 31388768 PMCID: PMC6733828 DOI: 10.1007/s00441-019-03075-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/08/2019] [Indexed: 12/14/2022]
Abstract
Digestive systems and extracellular digestion are key animal features, but their emergence during early animal evolution is currently poorly understood. As the last common ancestor of non-bilaterian animal groups (sponges, ctenophores, placozoans and cnidarians) dates back to the beginning of animal life, their study and comparison provides important insights into the early evolution of digestive systems and functions. Here, I have compiled an overview of the development and cell biology of digestive tissues in non-bilaterian animals. I will highlight the fundamental differences between extracellular and intracellular digestive processes, and how these are distributed among animals. Cnidarians (e.g. sea anemones, corals, jellyfish), the phylogenetic outgroup of bilaterians (e.g. vertebrates, flies, annelids), occupy a key position to reconstruct the evolution of bilaterian gut evolution. A major focus will therefore lie on the development and cell biology of digestive tissues in cnidarians, especially sea anemones, and how they compare to bilaterian gut tissues. In that context, I will also review how a recent study on the gastrula fate map of the sea anemone Nematostella vectensis challenges our long-standing conceptions on the evolution of cnidarian and bilaterian germ layers and guts.
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Affiliation(s)
- Patrick R H Steinmetz
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5006, Bergen, Norway.
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16
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Smith CL, Mayorova TD. Insights into the evolution of digestive systems from studies of Trichoplax adhaerens. Cell Tissue Res 2019; 377:353-367. [PMID: 31270610 DOI: 10.1007/s00441-019-03057-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/09/2019] [Indexed: 01/01/2023]
Abstract
Trichoplax, a member of the phylum Placozoa, is a tiny ciliated marine animal that glides on surfaces feeding on algae and cyanobacteria. It stands out from other animals in that it lacks an internal digestive system and, instead, digests food trapped under its lower surface. Here we review recent work on the phenotypes of its six cell types and their roles in digestion and feeding behavior. Phylogenomic analyses place Placozoa as sister to Eumetazoa, the clade that includes Cnidaria and Bilateria. Comparing the phenotypes of cells in Trichoplax to those of cells in the digestive epithelia of Eumetazoa allows us to make inferences about the cell types and mode of feeding of their ancestors. From our increasingly mechanistic understanding of feeding in Trichoplax, we get a glimpse into how primitive animals may have hunted and consumed food prior to the evolution of neurons, muscles, and internal digestive systems.
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Affiliation(s)
- Carolyn L Smith
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Tatiana D Mayorova
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
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17
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Nielsen C. Early animal evolution: a morphologist's view. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190638. [PMID: 31417759 PMCID: PMC6689584 DOI: 10.1098/rsos.190638] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/04/2019] [Indexed: 05/15/2023]
Abstract
Two hypotheses for the early radiation of the metazoans are vividly discussed in recent phylogenomic studies, the 'Porifera-first' hypothesis, which places the poriferans as the sister group of all other metazoans, and the 'Ctenophora-first' hypothesis, which places the ctenophores as the sister group to all other metazoans. It has been suggested that an analysis of morphological characters (including specific molecules) could throw additional light on the controversy, and this is the aim of this paper. Both hypotheses imply independent evolution of nervous systems in Planulozoa and Ctenophora. The Porifera-first hypothesis implies no homoplasies or losses of major characters. The Ctenophora-first hypothesis shows no important synapomorphies of Porifera, Planulozoa and Placozoa. It implies either independent evolution, in Planulozoa and Ctenophora, of a new digestive system with a gut with extracellular digestion, which enables feeding on larger organisms, or the subsequent loss of this new gut in the Poriferans (and the re-evolution of the collar complex). The major losses implied in the Ctenophora-first theory show absolutely no adaptational advantages. Thus, morphology gives very strong support for the Porifera-first hypothesis.
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Affiliation(s)
- Claus Nielsen
- The Natural History Museum of Denmark, University of Copenhagen, Zoological Museum, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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18
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Hare RM, Simmons LW. Sexual selection and its evolutionary consequences in female animals. Biol Rev Camb Philos Soc 2018; 94:929-956. [DOI: 10.1111/brv.12484] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Robin M. Hare
- Centre for Evolutionary Biology, School of Biological Sciences University of Western Australia 35 Stirling Highway, Perth, 6009 Australia
| | - Leigh W. Simmons
- Centre for Evolutionary Biology, School of Biological Sciences University of Western Australia 35 Stirling Highway, Perth, 6009 Australia
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19
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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: 27] [Impact Index Per Article: 4.5] [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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20
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Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus HJ, Krebs S, Vargas S, Blum H, Williams GA, Schierwater B, Wörheide G. Comparative genomics and the nature of placozoan species. PLoS Biol 2018; 16:e2005359. [PMID: 30063702 PMCID: PMC6067683 DOI: 10.1371/journal.pbio.2005359] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/28/2018] [Indexed: 12/30/2022] Open
Abstract
Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.
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Affiliation(s)
- Michael Eitel
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Warren R. Francis
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Frédérique Varoqueaux
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Hans-Jürgen Osigus
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gray A. Williams
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Hong Kong
| | - Bernd Schierwater
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology & Evolution, Yale University, New Haven, Connecticut, United States of America
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Staatliche Naturwissenschaftliche Sammlungen Bayerns (SNSB)–Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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21
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Miyazawa H, Nakano H. Multiple surveys employing a new sample-processing protocol reveal the genetic diversity of placozoans in Japan. Ecol Evol 2018; 8:2407-2417. [PMID: 29531663 PMCID: PMC5838039 DOI: 10.1002/ece3.3861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/19/2017] [Accepted: 01/02/2018] [Indexed: 11/08/2022] Open
Abstract
Placozoans, flat free-living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest-branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S rRNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, "ethanol-treated substrate sampling," for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine-jima, Chichi-jima, and Haha-jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine-jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.
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Affiliation(s)
- Hideyuki Miyazawa
- Shimoda Marine Research CenterUniversity of TsukubaShimodaShizuokaJapan
| | - Hiroaki Nakano
- Shimoda Marine Research CenterUniversity of TsukubaShimodaShizuokaJapan
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22
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Cuervo-González R. Rhodope placozophagus (Heterobranchia) a new species of turbellarian-like Gastropoda that preys on placozoans. ZOOL ANZ 2017. [DOI: 10.1016/j.jcz.2017.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Miranda LS, Hirano YM, Mills CE, Falconer A, Fenwick D, Marques AC, Collins AG. Systematics of stalked jellyfishes (Cnidaria: Staurozoa). PeerJ 2016; 4:e1951. [PMID: 27168970 PMCID: PMC4860332 DOI: 10.7717/peerj.1951] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/29/2016] [Indexed: 12/23/2022] Open
Abstract
Staurozoan classification is highly subjective, based on phylogeny-free inferences, and suborders, families, and genera are commonly defined by homoplasies. Additionally, many characters used in the taxonomy of the group have ontogenetic and intraspecific variation, and demand new and consistent assessments to establish their correct homologies. Consequently, Staurozoa is in need of a thorough systematic revision. The aim of this study is to propose a comprehensive phylogenetic hypothesis for Staurozoa, providing the first phylogenetic classification for the group. According to our working hypothesis based on a combined set of molecular data (mitochondrial markers COI and 16S, and nuclear markers ITS, 18S, and 28S), the traditional suborders Cleistocarpida (animals with claustrum) and Eleutherocarpida (animals without claustrum) are not monophyletic. Instead, our results show that staurozoans are divided into two groups, herein named Amyostaurida and Myostaurida, which can be distinguished by the absence/presence of interradial longitudinal muscles in the peduncle, respectively. We propose a taxonomic revision at the family and genus levels that preserves the monophyly of taxa. We provide a key for staurozoan genera and discuss the evolution of the main characters used in staurozoan taxonomy.
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Affiliation(s)
- Lucília S Miranda
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Yayoi M Hirano
- Coastal Branch of Natural History Museum and Institute, Chiba, Katsuura, Chiba, Japan
| | - Claudia E Mills
- Friday Harbor Laboratories and the Department of Biology, University of Washington, Friday Harbor, Washington, United States of America
| | - Audrey Falconer
- Marine Research Group of the Field Naturalists Club of Victoria, Melbourne, Victoria, Australia.,Sciences Department, Museum Victoria, Melbourne, Victoria, Australia
| | | | - Antonio C Marques
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, São Paulo, Brazil
| | - Allen G Collins
- National Systematics Laboratory, National Marine Fisheries Service (NMFS), National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
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24
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Schierwater B, Holland PWH, Miller DJ, Stadler PF, Wiegmann BM, Wörheide G, Wray GA, DeSalle R. Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Hale R, Strutt D. Conservation of Planar Polarity Pathway Function Across the Animal Kingdom. Annu Rev Genet 2015; 49:529-51. [DOI: 10.1146/annurev-genet-112414-055224] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosalind Hale
- Bateson Centre,
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - David Strutt
- Bateson Centre,
- Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
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26
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Paknia O, Schierwater B. Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa. PLoS One 2015; 10:e0140162. [PMID: 26580806 PMCID: PMC4651326 DOI: 10.1371/journal.pone.0140162] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/10/2015] [Indexed: 02/02/2023] Open
Abstract
The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km2 resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing “no biogeography.”
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Affiliation(s)
- Omid Paknia
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- * E-mail:
| | - Bernd Schierwater
- ITZ, Ecology and Evolution, TiHo Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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27
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Abstract
The non-bilaterian animals comprise organisms in the phyla Porifera, Cnidaria, Ctenophora and Placozoa. These early-diverging phyla are pivotal to understanding the evolution of bilaterian animals. After the exponential increase in research in evolutionary development (evo-devo) in the last two decades, these organisms are again in the spotlight of evolutionary biology. In this work, I briefly review some aspects of the developmental biology of nonbilaterians that contribute to understanding the evolution of development and of the metazoans. The evolution of the developmental genetic toolkit, embryonic polarization, the origin of gastrulation and mesodermal cells, and the origin of neural cells are discussed. The possibility that germline and stem cell lineages have the same origin is also examined. Although a considerable number of non-bilaterian species are already being investigated, the use of species belonging to different branches of non-bilaterian lineages and functional experimentation with gene manipulation in the majority of the non-bilaterian lineages will be necessary for further progress in this field.
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Affiliation(s)
- Emilio Lanna
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal da Bahia, Salvador, BA, Brazil
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28
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Lambertz M, Perry SF. Chordate phylogeny and the meaning of categorial ranks in modern evolutionary biology. Proc Biol Sci 2015; 282:20142327. [PMID: 25925098 DOI: 10.1098/rspb.2014.2327] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Markus Lambertz
- Institut für Zoologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, 53115 Bonn, Germany
| | - Steven F Perry
- Institut für Zoologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, 53115 Bonn, Germany
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29
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Nikitin M. Bioinformatic prediction of Trichoplax adhaerens regulatory peptides. Gen Comp Endocrinol 2015; 212:145-55. [PMID: 24747483 DOI: 10.1016/j.ygcen.2014.03.049] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 01/29/2023]
Abstract
Trichoplax adhaerens (phylum Placozoa) is a very simple organism that lacks a nervous system. However, its genome contains many genes essential for neuronal function and development. I report the results of regulatory peptide predictions for this enigmatic animal. Extensive transcriptome, genome, and predicted proteome mining allowed us to predict four insulins, at least five short peptide precursors, one granulin, one paracrine regulator of cell growth, and one complex temptin-attractin pheromone signaling system. The expression of three insulins, four short peptide precursors, granulin, and one out of the six temptin genes was detected. Five predicted regulatory peptide precursors could potentially release over 60 different mature peptides. Some of the predicted peptides are somewhat similar to anthozoan RW amides, Aplysia pedal peptide 3, and PRQFV amide. Other predicted short peptides could not readily be classified into established families. These data provide the foundation for the molecular, biochemical, physiological, and behavioral studies of one the most primitive animal coordination systems, and give unique insight into the origins and early evolution of the nervous system.
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Affiliation(s)
- Mikhail Nikitin
- Lomonosov Moscow State University, A.N. Belozersky Institute of Physico-chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow 119991, Russia.
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Suurväli J, Jouneau L, Thépot D, Grusea S, Pontarotti P, Du Pasquier L, Rüütel Boudinot S, Boudinot P. The Proto-MHC of Placozoans, a Region Specialized in Cellular Stress and Ubiquitination/Proteasome Pathways. THE JOURNAL OF IMMUNOLOGY 2014; 193:2891-901. [DOI: 10.4049/jimmunol.1401177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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31
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Bracken-Grissom H, Collins AG, Collins T, Crandall K, Distel D, Dunn C, Giribet G, Haddock S, Knowlton N, Martindale M, Medina M, Messing C, O'Brien SJ, Paulay G, Putnam N, Ravasi T, Rouse GW, Ryan JF, Schulze A, Wörheide G, Adamska M, Bailly X, Breinholt J, Browne WE, Diaz MC, Evans N, Flot JF, Fogarty N, Johnston M, Kamel B, Kawahara AY, Laberge T, Lavrov D, Michonneau F, Moroz LL, Oakley T, Osborne K, Pomponi SA, Rhodes A, Santos SR, Satoh N, Thacker RW, Van de Peer Y, Voolstra CR, Welch DM, Winston J, Zhou X. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. J Hered 2014; 105:1-18. [PMID: 24336862 DOI: 10.1093/jhered/est084] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.
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Nme family of proteins--clues from simple animals. Naunyn Schmiedebergs Arch Pharmacol 2014; 388:133-42. [PMID: 25042404 DOI: 10.1007/s00210-014-1017-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/02/2014] [Indexed: 01/08/2023]
Abstract
Nucleoside-diphosphate kinases (Nme/Nm23/NDPK) are evolutionarily conserved enzymes involved in many biological processes in vertebrates. The biochemical mechanisms of these processes are still largely unknown. The Nme family consists of ten members in humans of which Nme1/2 have been extensively studied in the context of carcinogenesis, especially metastasis formation. Lately, it has been proven that the majority of genes linked to human diseases were already present in species distantly related to humans. Most of cancer-related protein domains appeared during the two main evolutionary transitions-the emergence of unicellular eukaryotes and the transition to multicellular metazoans. In spite of these recent insights, current knowledge about cancer and status of cancer-related genes in simple animals is limited. One possible way of studying human diseases relies on analyzing genes/proteins that cause a certain disease by using model organism that represent the evolutionary level at which these genes have emerged. Therefore, basal metazoans are ideal model organisms for gaining a clearer picture how characteristics and functions of Nme genes changed in the transition to multicellularity and increasing complexity in animals, giving us exciting new evidence of their possible functions in potential pathological conditions in humans.
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Survey of the Japanese coast reveals abundant placozoan populations in the Northern Pacific Ocean. Sci Rep 2014; 4:5356. [PMID: 24942227 PMCID: PMC4062898 DOI: 10.1038/srep05356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/22/2014] [Indexed: 11/27/2022] Open
Abstract
Placozoans are the simplest extant free-living animals consisting of only five cell types and lacking neurons and muscle cells. Their phylogenetic position implies they are important for uncovering the origins of metazoans. Although recent studies show multiple groups within the phylum, most placozoan research has been performed on laboratory-cultured clones deriving from a single specimen. Reports of placozoan discovery are concentrated in the tropic and subtropic seas, especially in the Mediterranean and the Caribbean. Here, I report the unexpected abundance of placozoans from the Japanese coast. They were found from all six studied sites, even during winter for two sites, suggesting that they are more tolerant to low temperatures than previously regarded. These results suggest an unknown abundance of placozoans in the Northern Pacific Ocean and further studies on these populations may be essential in solving important biological problems of the phylum.
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Stampar SN, Maronna MM, Kitahara MV, Reimer JD, Morandini AC. Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly? PLoS One 2014; 9:e86612. [PMID: 24475157 PMCID: PMC3903554 DOI: 10.1371/journal.pone.0086612] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/12/2013] [Indexed: 11/19/2022] Open
Abstract
The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.
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Affiliation(s)
- Sérgio N. Stampar
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, Laboratório de Biologia Aquática - LABIA, Faculdade de Ciências e Letras de Assis, Departamento de Ciências Biológicas, Assis, São Paulo, Brazil
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, São Paulo, Brazil
| | - Maximiliano M. Maronna
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, São Paulo, Brazil
| | - Marcelo V. Kitahara
- Universidade de São Paulo, Centro de Biologia Marinha, São Sebastião, São Paulo, Brazil
| | - James D. Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - André C. Morandini
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, São Paulo, Brazil
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Abstract
Trichoplax adhaerens is an enigmatic basal animal with an extraordinarily simple morphological organization and surprisingly complex behaviors. Basic morphological, molecular and behavioral work is essential to better understand the unique and curious life style of these organisms. We provide basic instructions on how Trichoplax can be cultured and studied in the laboratory emphasizing behavioral and cellular aspects.
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Thacker RW, Hill AL, Hill MS, Redmond NE, Collins AG, Morrow CC, Spicer L, Carmack CA, Zappe ME, Pohlmann D, Hall C, Diaz MC, Bangalore PV. Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution. Integr Comp Biol 2013; 53:373-87. [PMID: 23748742 DOI: 10.1093/icb/ict071] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges.
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Affiliation(s)
- Robert W Thacker
- *Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA; Department of Biology, University of Richmond, Richmond, VA, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; School of Biological Sciences, MBC, 97 Lisburn Road, Queen's University, Belfast BT9 7BL, UK; Museo Marino de Margarita, Boulevard de Boca Del Rio, Boca del Rio, Nueva Esparta, Venezuela; **Department of Computer and Information Sciences, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA
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Eitel M, Osigus HJ, DeSalle R, Schierwater B. Global diversity of the Placozoa. PLoS One 2013; 8:e57131. [PMID: 23565136 PMCID: PMC3614897 DOI: 10.1371/journal.pone.0057131] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 01/17/2013] [Indexed: 11/18/2022] Open
Abstract
The enigmatic animal phylum Placozoa holds a key position in the metazoan Tree of Life. A simple bauplan makes it appear to be the most basal metazoan known and genetic evidence also points to a position close to the last common metazoan ancestor. Trichoplax adhaerens is the only formally described species in the phylum to date, making the Placozoa the only monotypic phylum in the animal kingdom. However, recent molecular genetic as well as morphological studies have identified a high level of diversity, and hence a potential high level of taxonomic diversity, within this phylum. Different taxa, possibly at different taxonomic levels, are awaiting description. In this review we firstly summarize knowledge on the morphology, phylogenetic position and ecology of the Placozoa. Secondly, we give an overview of placozoan morphological and genetic diversity and finally present an updated distribution of placozoan populations. We conclude that there is great potential and need to erect new taxa and to establish a firm system for this taxonomic tabula rasa.
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Affiliation(s)
- Michael Eitel
- Stiftung Tierärztliche Hochschule Hannover, Institut für Tierökologie und Zellbiologie, Ecology and Evolution, Hannover, Germany.
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38
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Dohrmann M, Wörheide G. Novel scenarios of early animal evolution--is it time to rewrite textbooks? Integr Comp Biol 2013; 53:503-11. [PMID: 23539635 DOI: 10.1093/icb/ict008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding how important phenotypic, developmental, and genomic features of animals originated and evolved is essential for many fields of biological research, but such understanding depends on robust hypotheses about the phylogenetic interrelationships of the higher taxa to which the studied species belong. Molecular approaches to phylogenetics have proven able to revolutionize our knowledge of organismal evolution. However, with respect to the deepest splits in the metazoan Tree of Life-the relationships between Bilateria and the four non-bilaterian phyla (Porifera, Placozoa, Ctenophora, and Cnidaria)-no consensus has been reached yet, since a number of different, often contradictory, hypotheses with sometimes spectacular implications have been proposed in recent years. Here, we review the recent literature on the topic and contrast it with more classical perceptions based on analyses of morphological characters. We conclude that the time is not yet ripe to rewrite zoological textbooks and advocate a conservative approach when it comes to developing scenarios of the early evolution of animals.
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Affiliation(s)
- Martin Dohrmann
- *Meiborssen 12, 37647 Vahlbruch, Germany; Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, 80333 München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 München, Germany; Bayerische Staatssammlung für Paläontologie und Geologie, 80333 München, Germany
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Abstract
Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.
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Affiliation(s)
- Nathaniel Evans
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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40
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Polyploidy and the evolution of complex traits. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2012; 2012:292068. [PMID: 22900230 PMCID: PMC3413983 DOI: 10.1155/2012/292068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/29/2012] [Accepted: 06/05/2012] [Indexed: 12/14/2022]
Abstract
We explore how whole-genome duplications (WGDs) may have given rise to complex innovations in cellular networks, innovations that could not have evolved through sequential single-gene duplications. We focus on two classical WGD events, one in bakers' yeast and the other at the base of vertebrates (i.e., two rounds of whole-genome duplication: 2R-WGD). Two complex adaptations are discussed in detail: aerobic ethanol fermentation in yeast and the rewiring of the vertebrate developmental regulatory network through the 2R-WGD. These two examples, derived from diverged branches on the eukaryotic tree, boldly underline the evolutionary potential of WGD in facilitating major evolutionary transitions. We close by arguing that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.
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Miyazawa H, Yoshida MA, Tsuneki K, Furuya H. Mitochondrial genome of a Japanese placozoan. Zoolog Sci 2012; 29:223-8. [PMID: 22468831 DOI: 10.2108/zsj.29.223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Placozoans are marine invertebrates found in tropical and subtropical waters. Their body plan is among the simplest of free-living animals. The present study determined the mitochondrial genome sequence of a placozoan collected on the coast of Shirahama, Wakayama, Honshu, Japan, and compared it with those of Trichoplax adhaerens from the Red Sea and of three strains from the Caribbean Sea. The sequences of mitochondrial respiratory chain of the Japanese placozoan genes are very similar to those of the BZ49 strain from the Caribbean Sea. However, there are distinct differences in gene arrangement, such as the location of two open reading frames. This Japanese placozoan is therefore distinguishable from the other strains. Based on current knowledge of placozoan 16S diversity our 'Shirahama' strain most likely represents the H15 lineage, known from the Philippines. In the mitochondrial genome of placozoans, substitution rates are slower than in bilaterians, whereas the rate of rearrangements is faster.
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Affiliation(s)
- Hideyuki Miyazawa
- Department of Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.
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42
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Eitel M, Guidi L, Hadrys H, Balsamo M, Schierwater B. New insights into placozoan sexual reproduction and development. PLoS One 2011; 6:e19639. [PMID: 21625556 PMCID: PMC3098260 DOI: 10.1371/journal.pone.0019639] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 04/13/2011] [Indexed: 11/18/2022] Open
Abstract
Unraveling animal life cycles and embryonic development is basic to understanding animal biology and often sheds light on phylogenetic relationships. A key group for understanding the evolution of the Metazoa is the early branching phylum Placozoa, which has attracted rapidly increasing attention. Despite over a hundred years of placozoan research the life cycle of this enigmatic phylum remains unknown. Placozoa are a unique model system for which the nuclear genome was published before the basic biology (i.e. life cycle and development) has been unraveled. Four organismal studies have reported the development of oocytes and one genetic study has nourished the hypothesis of sexual reproduction in natural populations at least in the past. Here we report new observations on sexual reproduction and embryonic development in the Placozoa and support the hypothesis of current sexual reproduction. The regular observation of oocytes and expressed sperm markers provide support that placozoans reproduce sexually in the field. Using whole genome and EST sequences and additional cDNA cloning we identified five conserved sperm markers, characteristic for different stages in spermatogenesis. We also report details on the embryonic development up to a 128-cell stage and new ultrastructural features occurring during early development. These results suggest that sperm and oocyte generation and maturation occur in different placozoans and that clonal lineages reproduce bisexually in addition to the standard mode of vegetative reproduction. The sum of observations is best congruent with the hypothesis of a simple life cycle with an alternation of reproductive modes between bisexual and vegetative reproduction.
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Affiliation(s)
- Michael Eitel
- Stiftung Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Hannover, Germany.
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43
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Edgecombe GD, Giribet G, Dunn CW, Hejnol A, Kristensen RM, Neves RC, Rouse GW, Worsaae K, Sørensen MV. Higher-level metazoan relationships: recent progress and remaining questions. ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0044-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Guidi L, Eitel M, Cesarini E, Schierwater B, Balsamo M. Ultrastructural analyses support different morphological lineages in the phylum Placozoa Grell, 1971. J Morphol 2011; 272:371-8. [PMID: 21246596 DOI: 10.1002/jmor.10922] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/01/2010] [Accepted: 10/03/2010] [Indexed: 11/12/2022]
Abstract
The morphology and ultrastructure of 10 clonal placozoan lineages were studied. We scored several morphological characters at a cellular and intracellular level and identified a number of morphological differences among clones. Some differences appear clone specific and allow recognizing five distinct lineages based on morphological criteria only. These data will be crucial for a yet to be established placozoan systematics. Furthermore, we here describe three new diagnostic morphological characters for Placozoa: a new structure in the upper epithelium, called "concave disc," two distinct subpopulations of fiber cells, and especially small cells in the body margin. Besides the fiber cells appear to be arranged in several layers forming a complex, three-dimensional net not previously described. We also describe the marginal cells as the formerly suggested potential stem-cell type. The basic morphology is revised.
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Affiliation(s)
- Loretta Guidi
- Dipartimento di Scienze dell'Uomo, dell'Ambiente e della Natura, Università degli Studi di Urbino Carlo Bo, Campus Scientifico, Località Crocicchia, 61029 Urbino, Italy.
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45
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Affiliation(s)
- Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.
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46
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Eitel M, Schierwater B. The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical waters. Mol Ecol 2010; 19:2315-27. [PMID: 20604867 DOI: 10.1111/j.1365-294x.2010.04617.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.
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Affiliation(s)
- M Eitel
- Tierärztliche Hochschule Hannover, ITZ, Ecology and Evolution, Hannover, Germany.
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47
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Sperling EA, Vinther J. A placozoan affinity for Dickinsonia and the evolution of late Proterozoic metazoan feeding modes. Evol Dev 2010; 12:201-9. [PMID: 20433459 DOI: 10.1111/j.1525-142x.2010.00404.x] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dickinsonia is one of the most recognizable forms in the Ediacaran fauna, but its phylogenetic position has been contentious, and it has been placed in almost every kingdom of life. Here, it is hypothesized that the affinities of Dickinsonia lie with the Placozoa (Metazoa), an understudied phylum that is widespread in tropical seas worldwide. Modern placozoans show obvious differences in size and axial organization compared with Dickinsonia, but these differences can be accounted for by the stem-group/crown-group distinction. The affinity with placozoans is evidenced primarily by the unique feeding mode of Dickinsonia, which is demonstrated by a series of feeding traces. These traces indicate that Dickinsonia moved over the Ediacaran matgrounds, and digested the mat using its entire lower sole. The ability of Dickinsonia to move negates an algal, fungal, or sponge affinity, while the feeding mode, external digestion with a ventral sole, rules out placement within any sponge or eumetazoan lineage. The only organisms that both move and feed in this manner are placozoans. Recent molecular phylogenetic studies have demonstrated that placozoans lie above sponges but below Eumetazoa. We hypothesize that Dickinsonia and other externally digesting Ediacaran forms are either stem-placozoans, or a series of extinct lineages above sponges and below eumetazoans on the metazoan tree. We discuss the potential evolutionary transitions between the main metazoan feeding modes in the context of the emerging molecular phylogeny, and suggest that aspects of the sponge and placozoan feeding strategies are relicts of nonuniformitarian Proterozoic ocean conditions.
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Affiliation(s)
- Erik A Sperling
- Department of Geology and Geophysics, Yale University, New Haven, CT 06520, USA.
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48
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes assembled from across the metazoan animals: Effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. Mol Phylogenet Evol 2010; 55:1-17. [DOI: 10.1016/j.ympev.2009.09.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 08/28/2009] [Accepted: 09/22/2009] [Indexed: 10/20/2022]
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49
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Gazave E, Lapébie P, Richards GS, Brunet F, Ereskovsky AV, Degnan BM, Borchiellini C, Vervoort M, Renard E. Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomes. BMC Evol Biol 2009; 9:249. [PMID: 19825158 PMCID: PMC2770060 DOI: 10.1186/1471-2148-9-249] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 10/13/2009] [Indexed: 12/20/2022] Open
Abstract
Background Of the 20 or so signal transduction pathways that orchestrate cell-cell interactions in metazoans, seven are involved during development. One of these is the Notch signalling pathway which regulates cellular identity, proliferation, differentiation and apoptosis via the developmental processes of lateral inhibition and boundary induction. In light of this essential role played in metazoan development, we surveyed a wide range of eukaryotic genomes to determine the origin and evolution of the components and auxiliary factors that compose and modulate this pathway. Results We searched for 22 components of the Notch pathway in 35 different species that represent 8 major clades of eukaryotes, performed phylogenetic analyses and compared the domain compositions of the two fundamental molecules: the receptor Notch and its ligands Delta/Jagged. We confirm that a Notch pathway, with true receptors and ligands is specific to the Metazoa. This study also sheds light on the deep ancestry of a number of genes involved in this pathway, while other members are revealed to have a more recent origin. The origin of several components can be accounted for by the shuffling of pre-existing protein domains, or via lateral gene transfer. In addition, certain domains have appeared de novo more recently, and can be considered metazoan synapomorphies. Conclusion The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa.
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Affiliation(s)
- Eve Gazave
- Aix-Marseille Universités, Centre d'Océanologie de Marseille, Station marine d'Endoume - CNRS UMR 6540-DIMAR, rue de Batterie des Lions, 13007 Marseille, France.
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50
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Leclère L, Schuchert P, Cruaud C, Couloux A, Manuel M. Molecular phylogenetics of Thecata (Hydrozoa, Cnidaria) reveals long-term maintenance of life history traits despite high frequency of recent character changes. Syst Biol 2009; 58:509-26. [PMID: 20525605 DOI: 10.1093/sysbio/syp044] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two fundamental life cycle types are recognized among hydrozoan cnidarians, the benthic (generally colonial) polyp stage either producing pelagic sexual medusae or directly releasing gametes elaborated from an attached gonophore. The existence of intermediate forms, with polyps producing simple medusoids, has been classically considered compelling evidence in favor of phyletic gradualism. In order to gain insights about the evolution of hydrozoan life history traits, we inferred phylogenetic relationships of 142 species of Thecata (= Leptothecata, Leptomedusae), the most species-rich hydrozoan group, using 3 different ribosomal RNA markers (16S, 18S, and 28S). In conflict with morphology-derived classifications, most thecate species fell in 2 well-supported clades named here Statocysta and Macrocolonia. We inferred many independent medusa losses among Statocysta. Several instances of secondary regain of medusoids (but not of full medusa) from medusa-less ancestors were supported among Macrocolonia. Furthermore, life cycle character changes were significantly correlated with changes affecting colony shape. For both traits, changes did not reflect graded and progressive loss or gain of complexity. They were concentrated in recent branches, with intermediate character states being relatively short lived at a large evolutionary scale. This punctuational pattern supports the existence of 2 alternative stable evolutionary strategies: simple stolonal colonies with medusae (the ancestral strategy, seen in most Statocysta species) versus large complex colonies with fixed gonophores (the derived strategy, seen in most Macrocolonia species). Hypotheses of species selection are proposed to explain the apparent long-term stability of these life history traits despite a high frequency of character change. Notably, maintenance of the medusa across geological time in Statocysta might be due to higher extinction rates for species that have lost this dispersive stage.
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Affiliation(s)
- Lucas Leclère
- Université Paris 06, UMR 7138/Centre National de la Recherche Scientifique UPMC MNHN IRD, 7 quai St Bernard, Paris, France.
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