1
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Evans SD, Hughes IV, Hughes EB, Dzaugis PW, Dzaugis MP, Gehling JG, García-Bellido DC, Droser ML. A new motile animal with implications for the evolution of axial polarity from the Ediacaran of South Australia. Evol Dev 2024:e12491. [PMID: 39228078 DOI: 10.1111/ede.12491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 08/06/2024] [Accepted: 08/19/2024] [Indexed: 09/05/2024]
Abstract
Fossils of the Ediacara Biota preserve the oldest evidence for complex, macroscopic animals. Most are difficult to constrain phylogenetically, however, the presence of rare, derived groups suggests that many more fossils from this period represent extant groups than are currently appreciated. One approach to recognize such early animals is to instead focus on characteristics widespread in animals today, for example multicellularity, motility, and axial polarity. Here, we describe a new taxon, Quaestio simpsonorum gen. et sp. nov. from the Ediacaran of South Australia. Quaestio is reconstructed with a thin external membrane connecting more resilient tissues with anterior-posterior polarity, left-right asymmetry and tentative evidence for dorsoventral differentiation. Associated trace fossils indicate an epibenthic and motile lifestyle. Our results suggest that Quaestio was a motile eumetazoan with a body plan not previously recognized in the Ediacaran, including definitive evidence of chirality. This organization, combined with previous evidence for axial patterning in a variety of other Ediacara taxa, demonstrates that metazoan body plans were well established in the Precambrian.
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Affiliation(s)
- Scott D Evans
- Earth, Ocean, and Atmospheric Sciences, Florida State University, Tallahassee, Florida, USA
| | - Ian V Hughes
- Organismic and Evolutionary Biology, Harvard, Cambridge, Massachusetts, USA
| | - Emily B Hughes
- Earth and Atmospheric Sciences, Georgia Tech, Atlanta, Georgia, USA
| | - Peter W Dzaugis
- Donald and Barbara Zucker School of Medicine, Hofstra University, Hempstead, New York, USA
| | | | - James G Gehling
- Earth Sciences, South Australian Museum, Adelaide, South Australia, Australia
| | - Diego C García-Bellido
- Earth Sciences, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Mary L Droser
- Earth and Planetary Sciences, University of California Riverside, Riverside, California, USA
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2
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Redmond AK. Acoelomorph flatworm monophyly is a long-branch attraction artefact obscuring a clade of Acoela and Xenoturbellida. Proc Biol Sci 2024; 291:20240329. [PMID: 39288803 PMCID: PMC11407873 DOI: 10.1098/rspb.2024.0329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/27/2024] [Accepted: 07/30/2024] [Indexed: 09/19/2024] Open
Abstract
Acoelomorpha is a broadly accepted clade of bilaterian animals made up of the fast-evolving, morphologically simple, mainly marine flatworm lineages Acoela and Nemertodermatida. Phylogenomic studies support Acoelomorpha's close relationship with the slowly evolving and similarly simplistic Xenoturbella, together forming the phylum Xenacoelomorpha. The phylogenetic placement of Xenacoelomorpha amongst bilaterians is controversial, with some studies supporting Xenacoelomorpha as the sister group to all other bilaterians, implying that their simplicity may be representative of early bilaterians. Others propose that this placement is an error resulting from the fast-evolving Acoelomorpha, and instead suggest that they are the degenerate sister group to Ambulacraria. Perhaps as a result of this debate, internal xenacoelomorph relationships have been somewhat overlooked at a phylogenomic scale. Here, I employ a highly targeted approach to detect and overcome possible phylogenomic error in the relationship between Xenoturbella and the fast-evolving acoelomorph flatworms. The results indicate that the subphylum Acoelomorpha is a long-branch attraction artefact obscuring a previously undiscovered clade comprising Xenoturbella and Acoela, which I name Xenacoela. The findings also suggest that Xenacoelomorpha is not the sister group to all other bilaterians. This study provides a template for future efforts aimed at discovering and correcting unrecognized long-branch attraction artefacts throughout the tree of life.
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3
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Liu H, Steenwyk JL, Zhou X, Schultz DT, Kocot KM, Shen XX, Rokas A, Li Y. A taxon-rich and genome-scale phylogeny of Opisthokonta. PLoS Biol 2024; 22:e3002794. [PMID: 39283949 DOI: 10.1371/journal.pbio.3002794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 09/26/2024] [Accepted: 08/07/2024] [Indexed: 09/27/2024] Open
Abstract
Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.
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Affiliation(s)
- Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Darrin T Schultz
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, United States of America
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Kevin M Kocot
- University of Alabama, Department of Biological Sciences & Alabama Museum of Natural History, Tuscaloosa, Alabama, United States of America
| | - Xing-Xing Shen
- Institute of Insect Sciences and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
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4
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Hookabe N, Jimi N, Furushima Y, Fujiwara Y. Discovery of deep-sea acoels from a chemosynthesis-based ecosystem. Biol Lett 2024; 20:20230573. [PMID: 39079676 PMCID: PMC11288667 DOI: 10.1098/rsbl.2023.0573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/03/2024] [Accepted: 06/05/2024] [Indexed: 08/03/2024] Open
Abstract
Chemosynthesis-based ecosystems such as hydrothermal vents and hydrocarbon seeps harbour various endemic species, each uniquely adapted to the extreme conditions. While some species rely on obligatory relationships with bacterial symbionts for nutrient uptake, scavengers and predators also play important roles in food web dynamics in these ecosystems. Acoels, members of the phylum Xenacoelomorpha, are simple, worm-like invertebrates found in marine environments worldwide but are scarcely understood taxa. This study presents a novel genus and species of acoel from a deep-sea hydrocarbon seep off Hatsushima, Japan, Hoftherma hatsushimaensis gen. et sp. nov. Our multi-locus phylogenetic analysis revealed that the acoels are nested within Hofsteniidae, a family previously known exclusively from shallow waters. This finding suggests that at least two independent colonization events occurred in the chemosynthesis-based environments from the phylum Xenoacoelomorpha, represented by hofsteniid acoels and Xenoturbella. Previous reports of hofsteniid species from low-oxygen and sulfide-rich environments, including intertidal habitats with decomposing leaves, in addition to H. hatsushimaensis gen. et sp. nov. from a deep-sea hydrocarbon seep, imply a common ancestral adaptation to sulfide-rich ecosystems within Hofsteniidae. Moreover, the sister relationship between solenofilomorphid acoels predominating in sulfide-rich habitats indicates common ancestral adaptation to sulfide-rich ecosystems between these two families.
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Affiliation(s)
- Natsumi Hookabe
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa237-0061, Japan
| | - Naoto Jimi
- Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba, Mie517-0004, Japan
- Centre for Marine & Coastal Studies, Universiti Sains Malaysia 11800 USM, Gelugor, Penang, Malaysia
| | - Yasuo Furushima
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa237-0061, Japan
| | - Yoshihiro Fujiwara
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa237-0061, Japan
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5
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Lin CY, Marlétaz F, Pérez-Posada A, Martínez-García PM, Schloissnig S, Peluso P, Conception GT, Bump P, Chen YC, Chou C, Lin CY, Fan TP, Tsai CT, Gómez Skarmeta JL, Tena JJ, Lowe CJ, Rank DR, Rokhsar DS, Yu JK, Su YH. Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution. PLoS Biol 2024; 22:e3002661. [PMID: 38829909 PMCID: PMC11175523 DOI: 10.1371/journal.pbio.3002661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/13/2024] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of 2 hemichordate species, Ptychodera flava and Schizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N = 23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into 2 chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes and that maintenance of the clusters are likely due to lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of 3 pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ferdinand Marlétaz
- Center for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alberto Pérez-Posada
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | | | - Paul Peluso
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Paul Bump
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Cindy Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Tzu-Pei Fan
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Chang-Tai Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - José Luis Gómez Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Christopher J. Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, California, United States of America
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
| | - David R. Rank
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Daniel S. Rokhsar
- Chan-Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- Molecular Genetics Unit, Okinawa Institute for Science and Technology, Onna, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
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6
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Robertson HE, Sebé-Pedrós A, Saudemont B, Loe-Mie Y, Zakrzewski AC, Grau-Bové X, Mailhe MP, Schiffer P, Telford MJ, Marlow H. Single cell atlas of Xenoturbella bocki highlights limited cell-type complexity. Nat Commun 2024; 15:2469. [PMID: 38503762 PMCID: PMC10951248 DOI: 10.1038/s41467-024-45956-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/07/2024] [Indexed: 03/21/2024] Open
Abstract
Phylogenetic analyses over the last two decades have united a few small, and previously orphan clades, the nematodermatids, acoels and xenoturbelids, into the phylum Xenacoelomorpha. Some phylogenetic analyses support a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria), while others suggest that Xenacoelomorpha may be sister to the rest of the Bilateria (Nephrozoa). An understanding of the cell type complements of Xenacoelomorphs is essential to assessing these alternatives as well as to our broader understanding of bilaterian cell type evolution. Employing whole organism single-cell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes and more broadly share muscle and gland cell similarities with other metazoans. Taken together, these data are consistent with broad homologies of animal gland, muscle, and neurons as well as more specific affinities between Xenoturbella and acoel gut and epidermal tissues, consistent with the monophyly of Xenacoelomorpha.
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Affiliation(s)
- Helen E Robertson
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Anne-C Zakrzewski
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marie-Pierre Mailhe
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Philipp Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Institute of Zoology, Section Developmental Biology, University of Cologne, Köln, Wormlab, Germany
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Heather Marlow
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA.
- (Epi)genomics of Animal Development Unit, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France.
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7
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Nakano H, Nakano A, Maeno A, Thorndyke MC. Induced spawning with gamete release from body ruptures during reproduction of Xenoturbella bocki. Commun Biol 2023; 6:172. [PMID: 36805023 PMCID: PMC9938242 DOI: 10.1038/s42003-023-04549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Xenoturbella is a marine invertebrate with a simple body plan, with recent phylogenomic studies suggesting that it forms the phylum Xenacoelomorpha together with the acoelomorphs. The phylogenetic position of the phylum is still under debate, whether it is an early branching bilaterian or a sister group to the Ambulacraria. Phylogenetic traits often appear during development, and larva resembling the cnidarian planula has been reported for Xenoturbella. However, subsequent developmental studies on Xenoturbella have been scarce. This is mainly due to the difficulties in collecting and keeping adult animals, resulting in the lack of data on the reproduction of the animal, such as the breeding season and the spawning pattern. Here we report on the reproduction of X. bocki and confirm that its breeding season is winter. Spawning induction resulted in gametes being released from body ruptures and not the mouth. No evidence supported the animal as a simultaneous hermaphrodite.
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Affiliation(s)
- Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan. .,Kristineberg Marine Research Station, University of Gothenburg, Kristineberg 566, Fiskebäckskil, 45178, Sweden.
| | - Ako Nakano
- grid.20515.330000 0001 2369 4728Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka 415-0025 Japan
| | - Akiteru Maeno
- grid.288127.60000 0004 0466 9350Cell Architecture Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540 Japan
| | - Michael C. Thorndyke
- grid.8761.80000 0000 9919 9582Kristineberg Marine Research Station, University of Gothenburg, Kristineberg 566, Fiskebäckskil, 45178 Sweden
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8
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Nanglu K, Cole SR, Wright DF, Souto C. Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development. Biol Rev Camb Philos Soc 2023; 98:316-351. [PMID: 36257784 DOI: 10.1111/brv.12908] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Selina R Cole
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - David F Wright
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - Camilla Souto
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,School of Natural Sciences & Mathematics, Stockton University, 101 Vera King Farris Dr, Galloway, NJ, 08205, USA
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9
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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10
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Petersen CP. Wnt signaling in whole-body regeneration. Curr Top Dev Biol 2023; 153:347-380. [PMID: 36967200 DOI: 10.1016/bs.ctdb.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Regeneration abilities are widespread among animals and select species can restore any body parts removed by wounds that sever the major body axes. This capability of whole-body regeneration as exemplified in flatworm planarians, Acoels, and Cnidarians involves initial responses to injury, the assessment of wound site polarization, determination of missing tissue and programming of blastema fate, and patterned outgrowth to restore axis content and proportionality. Wnt signaling drives many shared and conserved aspects of the biology of whole-body regeneration in the planarian species Schmidtea mediterranea and Dugesia japonica, in the Acoel Hofstenia miamia, and in Cnidarians Hydra and Nematostella. These overlapping mechanisms suggest whole-body regeneration might be an ancestral property across diverse animal taxa.
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Affiliation(s)
- Christian P Petersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Robert Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, United States.
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11
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Pisani D, Rossi ME, Marlétaz F, Feuda R. Phylogenomics: Is less more when using large-scale datasets? Curr Biol 2022; 32:R1340-R1342. [PMID: 36538883 DOI: 10.1016/j.cub.2022.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Phylogenetic studies have traditionally placed the simple Xenoacoelomorph worms as the sister group of all other animals with bilateral body symmetry. A new study shows that misidentification of orthologous genes might have been the source of at least some support for this placement.
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Affiliation(s)
- Davide Pisani
- Palaeobiology Research Group, School of Biological Sciences, University of Bristol, Bristol, UK; Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, UK.
| | - Maria Eleonora Rossi
- Palaeobiology Research Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Ferdinand Marlétaz
- Centre for Life's Origin & Evolution, Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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12
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Mulhair PO, McCarthy CGP, Siu-Ting K, Creevey CJ, O'Connell MJ. Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life. Curr Biol 2022; 32:5180-5188.e3. [PMID: 36356574 DOI: 10.1016/j.cub.2022.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/09/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022]
Abstract
Conflicting studies place a group of bilaterian invertebrates containing xenoturbellids and acoelomorphs, the Xenacoelomorpha, as either the primary emerging bilaterian phylum1,2,3,4,5,6 or within Deuterostomia, sister to Ambulacraria.7,8,9,10,11 Although their placement as sister to the rest of Bilateria supports relatively simple morphology in the ancestral bilaterian, their alternative placement within Deuterostomia suggests a morphologically complex ancestral bilaterian along with extensive loss of major phenotypic traits in the Xenacoelomorpha. Recent studies have questioned whether Deuterostomia should be considered monophyletic at all.10,12,13 Hidden paralogy and poor phylogenetic signal present a major challenge for reconstructing species phylogenies.14,15,16,17,18 Here, we assess whether these issues have contributed to the conflict over the placement of Xenacoelomorpha. We reanalyzed published datasets, enriching for orthogroups whose gene trees support well-resolved clans elsewhere in the animal tree.16 We find that most genes in previously published datasets violate incontestable clans, suggesting that hidden paralogy and low phylogenetic signal affect the ability to reconstruct branching patterns at deep nodes in the animal tree. We demonstrate that removing orthogroups that cannot recapitulate incontestable relationships alters the final topology that is inferred, while simultaneously improving the fit of the model to the data. We discover increased, but ultimately not conclusive, support for the existence of Xenambulacraria in our set of filtered orthogroups. At a time when we are progressing toward sequencing all life on the planet, we argue that long-standing contentious issues in the tree of life will be resolved using smaller amounts of better quality data that can be modeled adequately.19.
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Affiliation(s)
- Peter O Mulhair
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Charley G P McCarthy
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Karen Siu-Ting
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Christopher J Creevey
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, UK
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Research Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Computational and Molecular Evolutionary Biology Research Group, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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13
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Ceccolini F, Cianferoni F. A replacement name for Pelophila Dörjes, 1968 (Xenacoelomorpha: Acoela, Convolutidae). GRAELLSIA 2022. [DOI: 10.3989/graellsia.2022.v78.339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Se ha detectado un homónimo más moderno entre los Acoela (Xenacoelomorpha, Acoelomorpha) y se propone el siguiente nombre sustitutivo: Acoelopelophila Ceccolini & Cianferoni nom. nov. pro Pelophila Dörjes, 1968 nec Dejean, 1821. Se da también la siguiente nueva combinación: Acoelopelophila lutheri (Westblad, 1946) comb. nov.
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14
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Abstract
In his prominent book Regeneration (1901), T.H. Morgan's collected and synthesized theoretical and experimental findings from a diverse array of regenerating animals and plants. Through his endeavor, he introduced a new way to study regeneration and its evolution, setting a conceptual framework that still guides today's research and that embraces the contemporary evolutionary and developmental approaches.In the first part of the chapter, we summarize Morgan's major tenets and use it as a narrative thread to advocate interpreting regenerative biology through the theoretical tools provided by evolution and developmental biology, but also to highlight potential caveats resulting from the rapid proliferation of comparative studies and from the expansion of experimental laboratory models. In the second part, we review some experimental evo-devo approaches, highlighting their power and some of their interpretative dangers. Finally, in order to further understand the evolution of regenerative abilities, we portray an adaptive perspective on the evolution of regeneration and suggest a framework for investigating the adaptive nature of regeneration.
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Affiliation(s)
| | - Alexandre Alié
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France.
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15
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Bozzo M, Costa S, Obino V, Bachetti T, Marcenaro E, Pestarino M, Schubert M, Candiani S. Functional Conservation and Genetic Divergence of Chordate Glycinergic Neurotransmission: Insights from Amphioxus Glycine Transporters. Cells 2021; 10:cells10123392. [PMID: 34943900 PMCID: PMC8699752 DOI: 10.3390/cells10123392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and neurons, respectively. Only limited information is available on glycinergic neurotransmission in invertebrates, and the evolution of glycinergic neurotransmission is poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possess three glycine transporter genes. Two of these (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, whereas the third (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. GlyT2.2 expression is predominantly non-neural, whereas GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are differentially expressed, respectively, in neurons and glia. Vertebrate glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by a paralog-specific inversion of gene expression. Despite this genetic divergence between amphioxus and vertebrates, we found strong evidence for conservation in the role glycinergic neurotransmission plays during larval swimming, the implication being that the neural networks controlling the rhythmic movement of chordate bodies may be homologous.
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Affiliation(s)
- Matteo Bozzo
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
| | - Simone Costa
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Valentina Obino
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Tiziana Bachetti
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Emanuela Marcenaro
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Mario Pestarino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France;
| | - Simona Candiani
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
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16
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Moroz LL, Nikitin MA, Poličar PG, Kohn AB, Romanova DY. Evolution of glutamatergic signaling and synapses. Neuropharmacology 2021; 199:108740. [PMID: 34343611 PMCID: PMC9233959 DOI: 10.1016/j.neuropharm.2021.108740] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
Glutamate (Glu) is the primary excitatory transmitter in the mammalian brain. But, we know little about the evolutionary history of this adaptation, including the selection of l-glutamate as a signaling molecule in the first place. Here, we used comparative metabolomics and genomic data to reconstruct the genealogy of glutamatergic signaling. The origin of Glu-mediated communications might be traced to primordial nitrogen and carbon metabolic pathways. The versatile chemistry of L-Glu placed this molecule at the crossroad of cellular biochemistry as one of the most abundant metabolites. From there, innovations multiplied. Many stress factors or injuries could increase extracellular glutamate concentration, which led to the development of modular molecular systems for its rapid sensing in bacteria and archaea. More than 20 evolutionarily distinct families of ionotropic glutamate receptors (iGluRs) have been identified in eukaryotes. The domain compositions of iGluRs correlate with the origins of multicellularity in eukaryotes. Although L-Glu was recruited as a neuro-muscular transmitter in the early-branching metazoans, it was predominantly a non-neuronal messenger, with a possibility that glutamatergic synapses evolved more than once. Furthermore, the molecular secretory complexity of glutamatergic synapses in invertebrates (e.g., Aplysia) can exceed their vertebrate counterparts. Comparative genomics also revealed 15+ subfamilies of iGluRs across Metazoa. However, most of this ancestral diversity had been lost in the vertebrate lineage, preserving AMPA, Kainate, Delta, and NMDA receptors. The widespread expansion of glutamate synapses in the cortical areas might be associated with the enhanced metabolic demands of the complex brain and compartmentalization of Glu signaling within modular neuronal ensembles.
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Affiliation(s)
- Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Departments of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - 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
| | - Pavlin G Poličar
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA; Faculty of Computer and Information Science, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, St. Augustine, FL, 32080, USA
| | - Daria Y Romanova
- Cellular Neurobiology of Learning Lab, Institute of Higher Nervous Activity and Neurophysiology, Moscow, 117485, Russia.
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17
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Atherton S, Jondelius U. Phylogenetic assessment and systematic revision of the acoel family Isodiametridae. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Isodiametridae is a large family of Acoela with 22 nominal genera and nearly 100 species. Unfortunately, systematics of Isodiametridae, as it stands, is highly problematic. Genera frequently have been proposed without reference to an explicit phylogenetic hypothesis, such that the current classification system holds little or no predictive power. Many taxa do not fit with the family diagnosis, and it is increasingly difficult to determine in which taxon a new species should be described. Herein, we reconstruct the phylogenetic relationships of Acoela with a focus on Isodiametridae using both previously published and new ribosomal and mitochondrial sequence data. Our dataset comprises sequences from 45 species representing 16 of the 22 isodiametrid genera. Our results recovered a well-supported Isodiametridae, but provided further evidence that the family and several genera within require revision. We have updated the classification system of Isodiametridae to be consistent with its phylogeny, including the transference of Otocelis to Otocelididae, Postaphanostoma and Faerlea to Mecynostomidae and Alluna to Actinoposthiidae. Six other genera are placed in synonymy. We review the morphological taxonomy and provide an identification key of the genera in the revised family.
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Affiliation(s)
- Sarah Atherton
- Department of Zoology, Naturhistoriska riksmuseet, Stockholm, Sweden
| | - Ulf Jondelius
- Department of Zoology, Naturhistoriska riksmuseet, Stockholm, Sweden
- Department of Zoology, Systematics and Evolution, Stockholm Universitet, Stockholm, Sweden
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18
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Taubenheim J, Kortmann C, Fraune S. Function and Evolution of Nuclear Receptors in Environmental-Dependent Postembryonic Development. Front Cell Dev Biol 2021; 9:653792. [PMID: 34178983 PMCID: PMC8222990 DOI: 10.3389/fcell.2021.653792] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Nuclear receptors (NRs) fulfill key roles in the coordination of postembryonal developmental transitions in animal species. They control the metamorphosis and sexual maturation in virtually all animals and by that the two main environmental-dependent developmental decision points. Sexual maturation and metamorphosis are controlled by steroid receptors and thyroid receptors, respectively in vertebrates, while both processes are orchestrated by the ecdysone receptor (EcR) in insects. The regulation of these processes depends on environmental factors like nutrition, temperature, or photoperiods and by that NRs form evolutionary conserved mediators of phenotypic plasticity. While the mechanism of action for metamorphosis and sexual maturation are well studied in model organisms, the evolution of these systems is not entirely understood and requires further investigation. We here review the current knowledge of NR involvement in metamorphosis and sexual maturation across the animal tree of life with special attention to environmental integration and evolution of the signaling mechanism. Furthermore, we compare commonalities and differences of the different signaling systems. Finally, we identify key gaps in our knowledge of NR evolution, which, if sufficiently investigated, would lead to an importantly improved understanding of the evolution of complex signaling systems, the evolution of life history decision points, and, ultimately, speciation events in the metazoan kingdom.
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Affiliation(s)
- Jan Taubenheim
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Constantin Kortmann
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sebastian Fraune
- Zoology and Organismic Interactions, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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19
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Ziegler A, Sagorny C. Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach. BMC Biol 2021; 19:81. [PMID: 33888110 PMCID: PMC8063452 DOI: 10.1186/s12915-021-01000-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner. RESULTS Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories. CONCLUSIONS Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.
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Affiliation(s)
- Alexander Ziegler
- Institut für Evolutionsbiologie und Ökologie, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 1, 53121, Bonn, Germany.
| | - Christina Sagorny
- Institut für Evolutionsbiologie und Ökologie, Rheinische Friedrich-Wilhelms-Universität, An der Immenburg 1, 53121, Bonn, Germany
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20
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Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat Commun 2021; 12:1783. [PMID: 33741994 PMCID: PMC7979703 DOI: 10.1038/s41467-021-22074-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
Resolving the relationships between the major lineages in the animal tree of life is necessary to understand the origin and evolution of key animal traits. Sponges, characterized by their simple body plan, were traditionally considered the sister group of all other animal lineages, implying a gradual increase in animal complexity from unicellularity to complex multicellularity. However, the availability of genomic data has sparked tremendous controversy as some phylogenomic studies support comb jellies taking this position, requiring secondary loss or independent origins of complex traits. Here we show that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models. Testing on real datasets, we show a great improvement in model-fit that attenuates branching artefacts induced by systematic error. We reanalyse key datasets and show that partitioned phylogenomics does not support comb jellies as sister to other animals at either the supermatrix or partition-specific level.
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21
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Kapli P, Natsidis P, Leite DJ, Fursman M, Jeffrie N, Rahman IA, Philippe H, Copley RR, Telford MJ. Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria. SCIENCE ADVANCES 2021; 7:eabe2741. [PMID: 33741592 PMCID: PMC7978419 DOI: 10.1126/sciadv.abe2741] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/01/2021] [Indexed: 05/05/2023]
Abstract
The bilaterally symmetric animals (Bilateria) are considered to comprise two monophyletic groups, Protostomia (Ecdysozoa and the Lophotrochozoa) and Deuterostomia (Chordata and the Xenambulacraria). Recent molecular phylogenetic studies have not consistently supported deuterostome monophyly. Here, we compare support for Protostomia and Deuterostomia using multiple, independent phylogenomic datasets. As expected, Protostomia is always strongly supported, especially by longer and higher-quality genes. Support for Deuterostomia, however, is always equivocal and barely higher than support for paraphyletic alternatives. Conditions that cause tree reconstruction errors-inadequate models, short internal branches, faster evolving genes, and unequal branch lengths-coincide with support for monophyletic deuterostomes. Simulation experiments show that support for Deuterostomia could be explained by systematic error. The branch between bilaterian and deuterostome common ancestors is, at best, very short, supporting the idea that the bilaterian ancestor may have been deuterostome-like. Our findings have important implications for the understanding of early animal evolution.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalis Natsidis
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel J Leite
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian Fursman
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nadia Jeffrie
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Imran A Rahman
- Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK
| | - Hervé Philippe
- Station d'Ecologie Théorique et Expérimentale, UMR CNRS 5321, Université Paul Sabatier, 09200 Moulis, France
| | - Richard R Copley
- Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Sorbonne Université, CNRS, 06230 Villefranche-sur-mer, France
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution, and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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22
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Abstract
Hemichordates, along with echinoderms and chordates, belong to the lineage of bilaterians called the deuterostomes. Their phylogenetic position as an outgroup to chordates provides an opportunity to investigate the evolutionary origins of the chordate body plan and reconstruct ancestral deuterostome characters. The body plans of the hemichordates and chordates are organizationally divergent making anatomical comparisons very challenging. The developmental underpinnings of animal body plans are often more conservative than the body plans they regulate, and offer a novel data set for making comparisons between morphologically divergent body architectures. Here I review the hemichordate developmental data generated over the past 20 years that further test hypotheses of proposed morphological affinities between the two taxa, but also compare the conserved anteroposterior, dorsoventral axial patterning programs and germ layer specification programs. These data provide an opportunity to determine which developmental programs are ancestral deuterostome or bilaterian innovations, and which ones occurred in stem chordates or vertebrates representing developmental novelties of the chordate body plan.
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23
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Goffredi SK, Motooka C, Fike DA, Gusmão LC, Tilic E, Rouse GW, Rodríguez E. Mixotrophic chemosynthesis in a deep-sea anemone from hydrothermal vents in the Pescadero Basin, Gulf of California. BMC Biol 2021; 19:8. [PMID: 33455582 PMCID: PMC7812739 DOI: 10.1186/s12915-020-00921-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Numerous deep-sea invertebrates, at both hydrothermal vents and methane seeps, have formed symbiotic associations with internal chemosynthetic bacteria in order to harness inorganic energy sources typically unavailable to animals. Despite success in nearly all marine habitats and their well-known associations with photosynthetic symbionts, Cnidaria remain one of the only phyla present in the deep-sea without a clearly documented example of dependence on chemosynthetic symbionts. RESULTS A new chemosynthetic symbiosis between the sea anemone Ostiactis pearseae and intracellular bacteria was discovered at ~ 3700 m deep hydrothermal vents in the southern Pescadero Basin, Gulf of California. Unlike most sea anemones observed from chemically reduced habitats, this species was observed in and amongst vigorously venting fluids, side-by-side with the chemosynthetic tubeworm Oasisia aff. alvinae. Individuals of O. pearseae displayed carbon, nitrogen, and sulfur tissue isotope values suggestive of a nutritional strategy distinct from the suspension feeding or prey capture conventionally employed by sea anemones. Molecular and microscopic evidence confirmed the presence of intracellular SUP05-related bacteria housed in the tentacle epidermis of O. pearseae specimens collected from 5 hydrothermally active structures within two vent fields ~ 2 km apart. SUP05 bacteria (Thioglobaceae) dominated the O. pearseae bacterial community, but were not recovered from other nearby anemones, and were generally rare in the surrounding water. Further, the specific Ostiactis-associated SUP05 phylotypes were not detected in the environment, indicating a specific association. Two unusual candidate bacterial phyla (the OD1 and BD1-5 groups) appear to associate exclusively with O. pearseae and may play a role in symbiont sulfur cycling. CONCLUSION The Cnidarian Ostiactis pearseae maintains a physical and nutritional alliance with chemosynthetic bacteria. The mixotrophic nature of this symbiosis is consistent with what is known about other cnidarians and the SUP05 bacterial group, in that they both form dynamic relationships to succeed in nature. The advantages gained by appropriating metabolic and structural resources from each other presumably contribute to their striking abundance in the Pescadero Basin, at the deepest known hydrothermal vents in the Pacific Ocean.
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Affiliation(s)
| | | | | | | | | | - Greg W Rouse
- Scripps Institution of Oceanography, San Diego, CA, USA
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24
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Kapli P, Telford MJ. Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha. SCIENCE ADVANCES 2020; 6:eabc5162. [PMID: 33310849 PMCID: PMC7732190 DOI: 10.1126/sciadv.abc5162] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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25
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Czekanski‐Moir JE, Rundell RJ. Endless forms most stupid, icky, and small: The preponderance of noncharismatic invertebrates as integral to a biologically sound view of life. Ecol Evol 2020; 10:12638-12649. [PMID: 33304481 PMCID: PMC7713927 DOI: 10.1002/ece3.6892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 01/02/2023] Open
Abstract
Big, beautiful organisms are useful for biological education, increasing evolution literacy, and biodiversity conservation. But if educators gloss over the ubiquity of streamlined and miniaturized organisms, they unwittingly leave students and the public vulnerable to the idea that the primary evolutionary plot of every metazoan lineage is "progressive" and "favors" complexity. We show that simple, small, and intriguingly repulsive invertebrate animals provide a counterpoint to misconceptions about evolution. Our examples can be immediately deployed in biology courses and outreach. This context emphasizes that chordates are not the pinnacle of evolution. Rather, in the evolution of animals, miniaturization, trait loss, and lack of perfection are at least as frequent as their opposites. Teaching about invertebrate animals in a "tree thinking" context uproots evolution misconceptions (for students and the public alike), provides a mental scaffold for understanding all animals, and helps to cultivate future ambassadors and experts on these little-known, weird, and fascinating taxa.
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Affiliation(s)
- Jesse E. Czekanski‐Moir
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNYUSA
| | - Rebecca J. Rundell
- Department of Environmental and Forest BiologyState University of New York College of Environmental Science and ForestrySyracuseNYUSA
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Budd GE, Mann RP. Survival and selection biases in early animal evolution and a source of systematic overestimation in molecular clocks. Interface Focus 2020; 10:20190110. [PMID: 32637066 PMCID: PMC7333906 DOI: 10.1098/rsfs.2019.0110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/21/2022] Open
Abstract
Important evolutionary events such as the Cambrian Explosion have inspired many attempts at explanation: why do they happen when they do? What shapes them, and why do they eventually come to an end? However, much less attention has been paid to the idea of a 'null hypothesis'-that certain features of such diversifications arise simply through their statistical structure. Such statistical features also appear to influence our perception of the timing of these events. Here, we show in particular that study of unusually large clades leads to systematic overestimates of clade ages from some types of molecular clocks, and that the size of this effect may be enough to account for the puzzling mismatches seen between these molecular clocks and the fossil record. Our analysis of the fossil record of the late Ediacaran to Cambrian suggests that it is likely to be recording a true evolutionary radiation of the bilaterians at this time, and that explanations involving various sorts of cryptic origins for the bilaterians do not seem to be necessary.
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Affiliation(s)
- Graham E. Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
| | - Richard P. Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
- The Alan Turing Institute, London NW1 2DB, UK
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Curini-Galletti M, Artois T, Di Domenico M, Fontaneto D, Jondelius U, Jörger KM, Leasi F, Martínez A, Norenburg JL, Sterrer W, Todaro MA. Contribution of soft-bodied meiofaunal taxa to Italian marine biodiversity. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1786607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- M. Curini-Galletti
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - T. Artois
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - M. Di Domenico
- Center for Marine Studies, Universidade Federal do Paraná, Curitiba, Brazil
| | - D. Fontaneto
- Molecular Ecology Group, Water Research Institute - CNR, Verbania, Italy
| | - U. Jondelius
- Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - K. M. Jörger
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
| | - F. Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee, Chattanooga, TN, USA
| | - A. Martínez
- Molecular Ecology Group, Water Research Institute - CNR, Verbania, Italy
| | - J. L. Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution (USA), Washington, DC, USA
| | | | - M. A. Todaro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
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Yin J, Zhang C, Mirarab S. ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization. Bioinformatics 2020; 35:3961-3969. [PMID: 30903685 DOI: 10.1093/bioinformatics/btz211] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 01/11/2023] Open
Abstract
MOTIVATION Evolutionary histories can change from one part of the genome to another. The potential for discordance between the gene trees has motivated the development of summary methods that reconstruct a species tree from an input collection of gene trees. ASTRAL is a widely used summary method and has been able to scale to relatively large datasets. However, the size of genomic datasets is quickly growing. Despite its relative efficiency, the current single-threaded implementation of ASTRAL is falling behind the data growth trends is not able to analyze the largest available datasets in a reasonable time. RESULTS ASTRAL uses dynamic programing and is not trivially parallel. In this paper, we introduce ASTRAL-MP, the first version of ASTRAL that can exploit parallelism and also uses randomization techniques to speed up some of its steps. Importantly, ASTRAL-MP can take advantage of not just multiple CPU cores but also one or several graphics processing units (GPUs). The ASTRAL-MP code scales very well with increasing CPU cores, and its GPU version, implemented in OpenCL, can have up to 158× speedups compared to ASTRAL-III. Using GPUs and multiple cores, ASTRAL-MP is able to analyze datasets with 10 000 species or datasets with more than 100 000 genes in <2 days. AVAILABILITY AND IMPLEMENTATION ASTRAL-MP is available at https://github.com/smirarab/ASTRAL/tree/MP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- John Yin
- Department of Mathematics, University of California at San Diego, La Jolla, CA, USA
| | - Chao Zhang
- Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, CA, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California at San Diego, La Jolla, CA, USA
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Yañez-Guerra LA, Elphick MR. Evolution and Comparative Physiology of Luqin-Type Neuropeptide Signaling. Front Neurosci 2020; 14:130. [PMID: 32132900 PMCID: PMC7041311 DOI: 10.3389/fnins.2020.00130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/31/2020] [Indexed: 02/01/2023] Open
Abstract
Luqin is a neuropeptide that was discovered and named on account of its expression in left upper quadrant cells of the abdominal ganglion in the mollusc Aplysia californica. Subsequently, luqin-type peptides were identified as cardio-excitatory neuropeptides in other molluscs and a cognate receptor was discovered in the pond snail Lymnaea stagnalis. Phylogenetic analyses have revealed that orthologs of molluscan luqin-type neuropeptides occur in other phyla; these include neuropeptides in ecdysozoans (arthropods, nematodes) that have a C-terminal RYamide motif (RYamides) and neuropeptides in ambulacrarians (echinoderms, hemichordates) that have a C-terminal RWamide motif (RWamides). Furthermore, precursors of luqin-type neuropeptides typically have a conserved C-terminal motif containing two cysteine residues, although the functional significance of this is unknown. Consistent with the orthology of the neuropeptides and their precursors, phylogenetic and pharmacological studies have revealed that orthologous G-protein coupled receptors (GPCRs) mediate effects of luqin-type neuropeptides in spiralians, ecdysozoans, and ambulacrarians. Luqin-type signaling originated in a common ancestor of the Bilateria as a paralog of tachykinin-type signaling but, unlike tachykinin-type signaling, luqin-type signaling was lost in chordates. This may largely explain why luqin-type signaling has received less attention than many other neuropeptide signaling systems. However, insights into the physiological actions of luqin-type neuropeptides (RYamides) in ecdysozoans have been reported recently, with roles in regulation of feeding and diuresis revealed in insects and roles in regulation of feeding, egg laying, locomotion, and lifespan revealed in the nematode Caenorhabditis elegans. Furthermore, characterization of a luqin-type neuropeptide in the starfish Asterias rubens (phylum Echinodermata) has provided the first insights into the physiological roles of luqin-type signaling in a deuterostome. In conclusion, although luqin was discovered in Aplysia over 30 years ago, there is still much to be learnt about luqin-type neuropeptide signaling. This will be facilitated in the post-genomic era by the emerging opportunities for experimental studies on a variety of invertebrate taxa.
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Affiliation(s)
- Luis Alfonso Yañez-Guerra
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
| | - Maurice R Elphick
- School of Biological and Chemical Sciences, Faculty of Science and Engineering, Queen Mary University of London, London, United Kingdom
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30
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Erwin DH. The origin of animal body plans: a view from fossil evidence and the regulatory genome. Development 2020; 147:147/4/dev182899. [DOI: 10.1242/dev.182899] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ABSTRACT
The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.
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Affiliation(s)
- Douglas H. Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, PO Box 37012, Washington, DC 20013-7012, USA
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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31
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Martynov A, Lundin K, Picton B, Fletcher K, Malmberg K, Korshunova T. Multiple paedomorphic lineages of soft-substrate burrowing invertebrates: parallels in the origin of Xenocratena and Xenoturbella. PLoS One 2020; 15:e0227173. [PMID: 31940379 PMCID: PMC6961895 DOI: 10.1371/journal.pone.0227173] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/12/2019] [Indexed: 01/21/2023] Open
Abstract
Paedomorphosis is an important evolutionary force. It has previously been suggested that a soft-substrate sediment-dwelling (infaunal) environment facilitates paedomorphic evolution in marine invertebrates. However, until recently this proposal was never rigorously tested with robust phylogeny and broad taxon selection. Here, for the first time, we present a molecular phylogeny for a majority of the 21 families of one of the largest nudibranch subgroups (Aeolidacea) and show that the externally highly simplified vermiform nudibranch family, Pseudovermidae, with clearly defined paedomorphic traits and inhabiting a soft-substrata environment, is a sister group to the complex nudibranch family, Cumanotidae. We also report the rediscovery of one of the most enigmatic nudibranchs-Xenocratena suecica-on the Swedish and Norwegian coasts 70 years after it was first found. Xenocratena was described from the same location and environment in the Swedish Gullmar fjord as one of the most enigmatic vermiform organisms, Xenoturbella bocki, which represents either an original simple bilaterian body plan or secondary simplification of a more complex organisation. Our results show that Xenocratena suecica reveals an onset of parallel paedomorphic evolution so we have proposed the new family, Xenocratenidae fam. n., to accommodate the molecular and morphological disparities we discovered. The paedomorphic origin of another aeolidacean family, Embletoniidae, is also demonstrated for the first time. Thus, by presenting three independent lineages from non-closely related aeolidacean families, Xenocratenidae fam. n., Cumanotidae and Embletoniidae, we confirm with phylogenetic data that a soft-substrata burrowing-related environment strongly favours paedomorphic evolution. We suggest criteria to distinguish ancestral and derived characters in the context of modifications of ontogenetic cycles. Applying an evolutionary model of the soft substrate-driven multiple paedomorphic origin of several families of nudibranch molluscs we propose that it is plausible to extend this model to other marine invertebrates and suggest that the ancestral organisation of the enigmatic metazoan, Xenoturbella, might correspond to the larval part of a complex ancestral bilaterian ontogenetic cycle with sedentary/semi-sedentary adult stages and planula-like larval stages.
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Affiliation(s)
| | - Kennet Lundin
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Bernard Picton
- National Museums Northern Ireland, Holywood, Northern Ireland, United Kingdom
- Queen’s University, Belfast, Northern Ireland, United Kingdom
| | - Karin Fletcher
- Milltech Marine, Port Orchard, Washington, United States of America
| | - Klas Malmberg
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Aquatilis, Gothenburg, Sweden
| | - Tatiana Korshunova
- Zoological Museum, Moscow State University, Moscow, Russia
- Koltzov Institute of Developmental Biology RAS, Moscow, Russia
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32
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Tewari AG, Owen JH, Petersen CP, Wagner DE, Reddien PW. A small set of conserved genes, including sp5 and Hox, are activated by Wnt signaling in the posterior of planarians and acoels. PLoS Genet 2019; 15:e1008401. [PMID: 31626630 PMCID: PMC6821139 DOI: 10.1371/journal.pgen.1008401] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/30/2019] [Accepted: 09/05/2019] [Indexed: 11/19/2022] Open
Abstract
Wnt signaling regulates primary body axis formation across the Metazoa, with high Wnt signaling specifying posterior identity. Whether a common Wnt-driven transcriptional program accomplishes this broad role is poorly understood. We identified genes acutely affected after Wnt signaling inhibition in the posterior of two regenerative species, the planarian Schmidtea mediterranea and the acoel Hofstenia miamia, which are separated by >550 million years of evolution. Wnt signaling was found to maintain positional information in muscle and regional gene expression in multiple differentiated cell types. sp5, Hox genes, and Wnt pathway components are down-regulated rapidly after β-catenin RNAi in both species. Brachyury, a vertebrate Wnt target, also displays Wnt-dependent expression in Hofstenia. sp5 inhibits trunk gene expression in the tail of planarians and acoels, promoting separate tail-trunk body domains. A planarian posterior Hox gene, Post-2d, promotes normal tail regeneration. We propose that common regulation of a small gene set–Hox, sp5, and Brachyury–might underlie the widespread utilization of Wnt signaling in primary axis patterning across the Bilateria. How animals form and maintain their body axes is a fundamental topic in developmental biology. Wnt signaling is an important regulator of head-tail axis formation across animals, with high Wnt signaling specifying tail identity. In this study, we use two species that are separated by more than 550 million years of evolution, planarians and acoels, to find genes regulated by Wnt signaling in the tail broadly in the Bilateria. We identified a small conserved set of Wnt-regulated genes, including the transcription factor-encoding genes sp5 and Hox. This suggests that regulation of this gene set might be a key function of Wnt signaling in the tails of bilaterally symmetric animals. Inhibition of a planarian posterior Hox gene, Post-2d, by RNAi caused tail-regeneration defects. Inhibition of sp5 by RNAi revealed that it functions to restrict the expression of trunk genes in the tail of planarians and acoels. Since Wnt signaling activates both trunk and tail patterning gene expression in planarians, this suggests a mechanism by which Wnt signaling can establish separate trunk-tail body domains through regulation of sp5.
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Affiliation(s)
- Aneesha G. Tewari
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jared H. Owen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Christian P. Petersen
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Daniel E. Wagner
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Peter W. Reddien
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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Ueki T, Arimoto A, Tagawa K, Satoh N. Xenacoelomorph-Specific Hox Peptides: Insights into the Phylogeny of Acoels, Nemertodermatids, and Xenoturbellids. Zoolog Sci 2019; 36:395-401. [DOI: 10.2108/zs190045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/10/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Tatsuya Ueki
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi Hiroshima, Hiroshima 739-8526, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kuni Tagawa
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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34
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Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M. Acoel genome reveals the regulatory landscape of whole-body regeneration. Science 2019; 363:363/6432/eaau6173. [PMID: 30872491 DOI: 10.1126/science.aau6173] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm Hofstenia miamia, a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during Hofstenia regeneration. Combining egr inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.
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Affiliation(s)
- Andrew R Gehrke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Emily Neverett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Brandt
- Department of Chemistry, University of California, Berkeley, CA 94703, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Graham Ruby
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94703, USA
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. .,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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Andrikou C, Thiel D, Ruiz-Santiesteban JA, Hejnol A. Active mode of excretion across digestive tissues predates the origin of excretory organs. PLoS Biol 2019; 17:e3000408. [PMID: 31356592 PMCID: PMC6687202 DOI: 10.1371/journal.pbio.3000408] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/08/2019] [Accepted: 07/12/2019] [Indexed: 11/21/2022] Open
Abstract
Most bilaterian animals excrete toxic metabolites through specialized organs, such as nephridia and kidneys, which share morphological and functional correspondences. In contrast, excretion in non-nephrozoans is largely unknown, and therefore the reconstruction of ancestral excretory mechanisms is problematic. Here, we investigated the excretory mode of members of the Xenacoelomorpha, the sister group to Nephrozoa, and Cnidaria, the sister group to Bilateria. By combining gene expression, inhibitor experiments, and exposure to varying environmental ammonia conditions, we show that both Xenacoelomorpha and Cnidaria are able to excrete across digestive-associated tissues. However, although the cnidarian Nematostella vectensis seems to use diffusion as its main excretory mode, the two xenacoelomorphs use both active transport and diffusion mechanisms. Based on these results, we propose that digestive-associated tissues functioned as excretory sites before the evolution of specialized organs in nephrozoans. We conclude that the emergence of a compact, multiple-layered bilaterian body plan necessitated the evolution of active transport mechanisms, which were later recruited into the specialized excretory organs.
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Affiliation(s)
- Carmen Andrikou
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Daniel Thiel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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36
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Marlétaz F. Zoology: Worming into the Origin of Bilaterians. Curr Biol 2019; 29:R577-R579. [DOI: 10.1016/j.cub.2019.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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37
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Gavilán B, Sprecher SG, Hartenstein V, Martinez P. The digestive system of xenacoelomorphs. Cell Tissue Res 2019; 377:369-382. [PMID: 31093756 DOI: 10.1007/s00441-019-03038-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 11/26/2022]
Abstract
Interest in the study of Xenacoelomorpha has recently been revived due to realization of its key phylogenetic position as the putative sister group of the remaining Bilateria. Phylogenomic studies have attracted the attention of researchers interested in the evolution of animals and the origin of novelties. However, it is clear that a proper understanding of novelties can only be gained in the context of thorough descriptions of the anatomy of the different members of this phylum. A considerable literature, based mainly on conventional histological techniques, describes different aspects of xenacoelomorphs' tissue architecture. However, the focus has been somewhat uneven; some tissues, such as the neuro-muscular system, are relatively well described in most groups, whereas others, including the digestive system, are only poorly understood. Our lack of knowledge of the xenacoelomorph digestive system is exacerbated by the assumption that, at least in Acoela, which possess a syncytial gut, the digestive system is a derived and specialized tissue with little bearing on what is observed in other bilaterian animals. Here, we try to remedy this lack of attention by revisiting the different studies of the xenacoelomorph digestive system, and we discuss the diversity present in the light of new evolutionary knowledge.
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Affiliation(s)
- B Gavilán
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
| | - S G Sprecher
- Department of Biology, University of Fribourg, 10, ch. Du Musée, 1700, Fribourg, Switzerland
| | - V Hartenstein
- Department of Biology, University of California, Los Angeles, CA, USA.
| | - P Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria. Curr Biol 2019; 29:1818-1826.e6. [PMID: 31104936 DOI: 10.1016/j.cub.2019.04.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/19/2019] [Accepted: 04/03/2019] [Indexed: 01/21/2023]
Abstract
Xenoturbella and the acoelomorph worms (Xenacoelomorpha) are simple marine animals with controversial affinities. They have been placed as the sister group of all other bilaterian animals (Nephrozoa hypothesis), implying their simplicity is an ancient characteristic [1, 2]; alternatively, they have been linked to the complex Ambulacraria (echinoderms and hemichordates) in a clade called the Xenambulacraria [3-5], suggesting their simplicity evolved by reduction from a complex ancestor. The difficulty resolving this problem implies the phylogenetic signal supporting the correct solution is weak and affected by inadequate modeling, creating a misleading non-phylogenetic signal. The idea that the Nephrozoa hypothesis might be an artifact is prompted by the faster molecular evolutionary rate observed within the Acoelomorpha. Unequal rates of evolution are known to result in the systematic artifact of long branch attraction, which would be predicted to result in an attraction between long-branch acoelomorphs and the outgroup, pulling them toward the root [6]. Other biases inadequately accommodated by the models used can also have strong effects, exacerbated in the context of short internal branches and long terminal branches [7]. We have assembled a large and informative dataset to address this problem. Analyses designed to reduce or to emphasize misleading signals show the Nephrozoa hypothesis is supported under conditions expected to exacerbate errors, and the Xenambulacraria hypothesis is preferred in conditions designed to reduce errors. Our reanalyses of two other recently published datasets [1, 2] produce the same result. We conclude that the Xenacoelomorpha are simplified relatives of the Ambulacraria.
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Ortega-Hernández J, Janssen R, Budd GE. The last common ancestor of Ecdysozoa had an adult terminal mouth. ARTHROPOD STRUCTURE & DEVELOPMENT 2019; 49:155-158. [PMID: 30458236 DOI: 10.1016/j.asd.2018.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
The Ecdysozoa is a major animal clade whose main uniting feature is a distinctive growth strategy that requires the periodical moulting of the external cuticle. The staggering diversity within Ecdysozoa has prompted substantial efforts to reconstruct their origin and early evolution. Based on palaentological and developmental data, we proposed a scenario for the early evolution of the ecdysozoan clade Panarthropoda (Onychophora, Tardigrada, Euarthropoda), and postulated that a terminal mouth is ancestral for this lineage. In light of the accompanying comment by Claus Nielsen, we take this opportunity to clarify the significance of our argumentation for Panarthropoda in the phylogenetic context of Ecdysozoa, and Bilateria more broadly. We conclude that the ancestral ecdysozoan most likely had an adult terminal mouth, and that the last common ancestors of all the phyla that constitute Ecdysozoa almost certainly also had an adult terminal mouth. The occurrence of a ventral-facing mouth in various adult ecdysozoans - particularly panarthropods - is the result of convergence. Despite the paucity of embryological data on fossil taxa, we contemplate the likelihood that a developmentally early ventral mouth opening could be ancestral for Ecdysozoa, and if so, then this would represent a symplesiomorphy of Bilateria as a whole.
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Affiliation(s)
- Javier Ortega-Hernández
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK; Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala se 752 36, Sweden
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala se 752 36, Sweden
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Nakano H, Miyazawa H. A New Species of Orthonectida That Parasitizes Xenoturbella bocki: Implications for Studies on Xenoturbella. THE BIOLOGICAL BULLETIN 2019; 236:66-73. [PMID: 30707607 DOI: 10.1086/700834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Orthonectida is a phylum of marine invertebrates known to parasitize many invertebrate animals. Because of its simple body plan, it was suggested that it belong to Mesozoa, together with Dicyemida, and that it represent the evolutionary step between unicellular organisms and multicellular animals. Recent studies, including analyses of its genomes, have clarified its phylogenetic position as a member of the Protostomia, but details such as the species diversity within the phylum and how it infects the host remain unknown. Here we report orthonectids discovered from the marine worm Xenoturbella bocki. Orthonectids were found from sections of four xenoturbellid specimens, collected eight years apart. Live females were also discovered on three separate occasions. These recurring instances of orthonectids found from Xenoturbella show that they are parasitic to the animal and not just chance contaminations. Based on morphological characters such as the presence of sexual dimorphism, the arrangement of oocytes within the female body, and the presence of crystalline inclusions in the male epidermal cells, we regard this orthonectid as a new species, Rhopalura xenoturbellae sp. nov. Since orthonectids are present within the xenoturbellid adult body, caution is needed when interpreting morphological, molecular, and experimental data from X. bocki. Further studies on R. xenoturbellae will yield important information on the fundamental biological details of orthonectids that remain unknown.
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Li Y, Kocot KM, Tassia MG, Cannon JT, Bernt M, Halanych KM. Mitogenomics Reveals a Novel Genetic Code in Hemichordata. Genome Biol Evol 2019; 11:29-40. [PMID: 30476024 PMCID: PMC6319601 DOI: 10.1093/gbe/evy254] [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] [Accepted: 11/20/2018] [Indexed: 01/26/2023] Open
Abstract
The diverse array of codon reassignments demonstrate that the genetic code is not universal in nature. Exploring mechanisms underlying codon reassignment is critical for understanding the evolution of the genetic code during translation. Hemichordata, comprising worm-like Enteropneusta and colonial filter-feeding Pterobranchia, is the sister taxon of echinoderms and is more distantly related to chordates. However, only a few hemichordate mitochondrial genomes have been sequenced, hindering our understanding of mitochondrial genome evolution within Deuterostomia. In this study, we sequenced four mitochondrial genomes and two transcriptomes, including representatives of both major hemichordate lineages and analyzed together with public available data. Contrary to the current understanding of the mitochondrial genetic code in hemichordates, our comparative analyses suggest that UAA encodes Tyr instead of a "Stop" codon in the pterobranch lineage Cephalodiscidae. We also predict that AAA encodes Lys in pterobranch and enteropneust mitochondrial genomes, contradicting the previous assumption that hemichordates share the same genetic code with echinoderms for which AAA encodes Asn. Thus, we propose a new mitochondrial genetic code for Cephalodiscus and a revised code for enteropneusts. Moreover, our phylogenetic analyses are largely consistent with previous phylogenomic studies. The only exception is the phylogenetic position of the enteropneust Stereobalanus, whose placement as sister to all other described enteropneusts. With broader taxonomic sampling, we provide evidence that evolution of mitochondrial gene order and genetic codes in Hemichordata are more dynamic than previously thought and these findings provide insights into mitochondrial genome evolution within this clade.
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Affiliation(s)
- Yuanning Li
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Kevin M Kocot
- Department of Biological Sciences & Alabama Museum of Natural History, The University of Alabama
| | - Michael G Tassia
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
| | - Johanna T Cannon
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara
| | - Matthias Bernt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Kenneth M Halanych
- Department of Biological Sciences & Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University
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Formery L, Schubert M, Croce JC. Ambulacrarians and the Ancestry of Deuterostome Nervous Systems. Results Probl Cell Differ 2019; 68:31-59. [PMID: 31598852 DOI: 10.1007/978-3-030-23459-1_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The evolutionary origin and history of metazoan nervous systems has been at the heart of numerous scientific debates for well over a century. This has been a particularly difficult issue to resolve within the deuterostomes, chiefly due to the distinct neural architectures observed within this group of animals. Indeed, deuterosomes feature central nervous systems, apical organs, nerve cords, and basiepidermal nerve nets. Comparative analyses investigating the anatomy and molecular composition of deuterostome nervous systems have nonetheless succeeded in identifying a number of shared and derived features. These analyses have led to the elaboration of diverse theories about the origin and evolutionary history of deuterostome nervous systems. Here, we provide an overview of these distinct theories. Further, we argue that deciphering the adult nervous systems of representatives of all deuterostome phyla, including echinoderms, which have long been neglected in this type of surveys, will ultimately provide answers to the questions concerning the ancestry and evolution of deuterostome nervous systems.
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Affiliation(s)
- Laurent Formery
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France
| | - Michael Schubert
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France
| | - Jenifer C Croce
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Evolution of Intercellular Signaling in Development (EvoInSiDe) Team, Villefranche-sur-Mer, France.
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Buckland-Nicks J, Lundin K, Wallberg A. The sperm of Xenacoelomorpha revisited: implications for the evolution of early bilaterians. ZOOMORPHOLOGY 2018. [DOI: 10.1007/s00435-018-0425-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Xiang P, Wang Y, Chen R, Zhao L, Wang C, Lin M. A bathypelagic ostracod Conchoecissa nigromaculatus sp. nov. (Myodocopa, Halocyprididae) from the South China Sea. PeerJ 2018; 6:e5557. [PMID: 30210944 PMCID: PMC6130238 DOI: 10.7717/peerj.5557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
Pelagic ostracods are one of the main groups of zooplankton and are abundant in marine ecosystems worldwide. The record of marine planktonic ostracod species in the central and southern part of the South China Sea accounts over for one-third of the total recorded marine planktonic ostracods in seas around China. In this study, we examined and compared the specimens from a recent cruise in this region that appeared to be different from previously described species of genus Conchoecissa, and then confirmed them as a new bathypelagic species Conchoecissa nigromaculatus. These specimens clearly differed from the other species of genus Conchoecissa with differences observed in the size, carapace, locations of glands, mandible, maxilla, sixth limb, and furca. In this species, mandibular coxal endite has no ventral finger process, maxilla has prominently large endites and has only two claws on the tip, the sixth limb has very simple endites, and this species has distinctive features not previously observed in the tribe Conchoeciini before. It is therefore necessary to emend the diagnosis of this group.
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Affiliation(s)
- Peng Xiang
- School of Life Science and Technology, Tongji University, Shanghai, China
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
| | - Yu Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
| | - Ruixiang Chen
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
| | - Liyuan Zhao
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
| | - Chunguang Wang
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
| | - Mao Lin
- Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, SOA, Xiamen, China
- Collaborative Innovation Center of Deep Sea Biology, Hangzhou, China
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Jehn J, Gebert D, Pipilescu F, Stern S, Kiefer JST, Hewel C, Rosenkranz D. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun Biol 2018; 1:137. [PMID: 30272016 PMCID: PMC6128900 DOI: 10.1038/s42003-018-0141-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Frank Pipilescu
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Sarah Stern
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Julian Simon Thilo Kiefer
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.
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Brauchle M, Bilican A, Eyer C, Bailly X, Martínez P, Ladurner P, Bruggmann R, Sprecher SG. Xenacoelomorpha Survey Reveals That All 11 Animal Homeobox Gene Classes Were Present in the First Bilaterians. Genome Biol Evol 2018; 10:2205-2217. [PMID: 30102357 PMCID: PMC6125248 DOI: 10.1093/gbe/evy170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2018] [Indexed: 11/13/2022] Open
Abstract
Homeodomain transcription factors are involved in many developmental processes across animals and have been linked to body plan evolution. Detailed classifications of these proteins identified 11 distinct classes of homeodomain proteins in animal genomes, each harboring specific sequence composition and protein domains. Although humans contain the full set of classes, Drosophila melanogaster and Caenorhabditis elegans each lack one specific class. Furthermore, representative previous analyses in sponges, ctenophores, and cnidarians could not identify several classes in those nonbilaterian metazoan taxa. Consequently, it is currently unknown when certain homeodomain protein classes first evolved during animal evolution. Here, we investigate representatives of the sister group to all remaining bilaterians, the Xenacoelomorpha. We analyzed three acoel, one nemertodermatid, and one Xenoturbella transcriptomes and identified their expressed homeodomain protein content. We report the identification of representatives of all 11 classes of animal homeodomain transcription factors in Xenacoelomorpha and we describe and classify their homeobox genes relative to the established animal homeodomain protein families. Our findings suggest that the genome of the last common ancestor of bilateria contained the full set of these gene classes, supporting the subsequent diversification of bilaterians.
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Affiliation(s)
- Michael Brauchle
- Department of Biology, Institute of Zoology, University of Fribourg, Switzerland.,Department of Biology, Institute of Cell Biology, University of Bern, Switzerland.,These authors contributed equally to this work
| | - Adem Bilican
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland.,These authors contributed equally to this work
| | - Claudia Eyer
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland
| | - Xavier Bailly
- UPMC-CNRS FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Pedro Martínez
- Departament de Genètica, Universitat de Barcelona, Catalonia, Spain.,Institut Català de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
| | - Peter Ladurner
- Institute of Zoology and Center of Molecular Bioscience Innsbruck, University of Innsbruck, Austria
| | - Rémy Bruggmann
- Department of Biology, Interfaculty Bioinformatics Unit, University of Bern, Switzerland
| | - Simon G Sprecher
- Department of Biology, Institute of Zoology, University of Fribourg, Switzerland
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Shekhar S, Roch S, Mirarab S. Species Tree Estimation Using ASTRAL: How Many Genes Are Enough? IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:1738-1747. [PMID: 28976320 DOI: 10.1109/tcbb.2017.2757930] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted gene tree topologies is ASTRAL. In this paper, we derive theoretical sample complexity results for the number of genes required by ASTRAL to guarantee reconstruction of the correct species tree with high probability. We also validate those theoretical bounds in a simulation study. Our results indicate that ASTRAL requires gene trees to reconstruct the species tree correctly with high probability where is the number of species and is the length of the shortest branch in the species tree. Our simulations, some under the anomaly zone, show trends consistent with the theoretical bounds and also provide some practical insights on the conditions where ASTRAL works well.
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48
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Thiel D, Franz-Wachtel M, Aguilera F, Hejnol A. Xenacoelomorph Neuropeptidomes Reveal a Major Expansion of Neuropeptide Systems during Early Bilaterian Evolution. Mol Biol Evol 2018. [PMCID: PMC6188537 DOI: 10.1093/molbev/msy160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neuropeptides are neurosecretory signaling molecules in protostomes and deuterostomes (together Nephrozoa). Little, however, is known about the neuropeptide complement of the sister group of Nephrozoa, the Xenacoelomorpha, which together form the Bilateria. Because members of the xenacoelomorph clades Xenoturbella, Nemertodermatida, and Acoela differ extensively in their central nervous system anatomy, the reconstruction of the xenacoelomorph and bilaterian neuropeptide complements may provide insights into the relationship between nervous system evolution and peptidergic signaling. Here, we analyzed transcriptomes of seven acoels, four nemertodermatids, and two Xenoturbella species using motif searches, similarity searches, mass spectrometry and phylogenetic analyses to characterize neuropeptide precursors and neuropeptide receptors. Our comparison of these repertoires with previously reported nephrozoan and cnidarian sequences shows that the majority of annotated neuropeptide GPCRs in cnidarians are not orthologs of specific bilaterian neuropeptide receptors, which suggests that most of the bilaterian neuropeptide systems evolved after the cnidarian–bilaterian evolutionary split. This expansion of more than 20 peptidergic systems in the stem leading to the Bilateria predates the evolution of complex nephrozoan organs and nervous system architectures. From this ancient set of neuropeptides, acoels show frequent losses that correlate with their divergent central nervous system anatomy. We furthermore detected the emergence of novel neuropeptides in xenacoelomorphs and their expansion along the nemertodermatid and acoel lineages, the two clades that evolved nervous system condensations. Together, our study provides fundamental insights into the early evolution of the bilaterian peptidergic systems, which will guide future functional and comparative studies of bilaterian nervous systems.
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Affiliation(s)
- Daniel Thiel
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | | | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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50
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Evolution of the bilaterian mouth and anus. Nat Ecol Evol 2018; 2:1358-1376. [PMID: 30135501 DOI: 10.1038/s41559-018-0641-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.
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