1
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Mapalo MA, Wolfe JM, Ortega-Hernández J. Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades. Commun Biol 2024; 7:953. [PMID: 39107512 PMCID: PMC11303527 DOI: 10.1038/s42003-024-06643-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
Tardigrades are a diverse phylum of microscopic invertebrates widely known for their extreme survival capabilities. Molecular clocks suggest that tardigrades diverged from other panarthropods before the Cambrian, but their fossil record is extremely sparse. Only the fossil tardigrades Milnesium swolenskyi (Late Cretaceous) and Paradoryphoribius chronocaribbeus (Miocene) have resolved taxonomic positions, restricting the availability of calibration points for estimating for the origin of this phylum. Here, we revise two crown-group tardigrades from Canadian Cretaceous-aged amber using confocal fluorescence microscopy, revealing critical morphological characters that resolve their taxonomic positions. Formal morphological redescription of Beorn leggi reveals that it features Hypsibius-type claws. We also describe Aerobius dactylus gen. et sp. nov. based on its unique combination of claw characters. Phylogenetic analyses indicate that Beo. leggi and Aer. dactylus belong to the eutardigrade superfamily Hypsibioidea, adding a critical fossil calibration point to investigate tardigrade origins. Our molecular clock estimates suggest an early Paleozoic diversification of crown-group Tardigrada and highlight the importance of Beo. leggi as a calibration point that directly impacts estimates of shallow nodes. Our results suggest that independent terrestrialization of eutardigrades and heterotardigrades occurred around the end-Carboniferous and Lower Jurassic, respectively. These estimates also provide minimum ages for convergent acquisition of cryptobiosis.
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Affiliation(s)
- Marc A Mapalo
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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2
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Campli G, Volovych O, Kim K, Veldsman WP, Drage HB, Sheizaf I, Lynch S, Chipman AD, Daley AC, Robinson-Rechavi M, Waterhouse RM. The moulting arthropod: a complete genetic toolkit review. Biol Rev Camb Philos Soc 2024. [PMID: 39039636 DOI: 10.1111/brv.13123] [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: 01/14/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Exoskeletons are a defining character of all arthropods that provide physical support for their segmented bodies and appendages as well as protection from the environment and predation. This ubiquitous yet evolutionarily variable feature has been instrumental in facilitating the adoption of a variety of lifestyles and the exploitation of ecological niches across all environments. Throughout the radiation that produced the more than one million described modern species, adaptability afforded by segmentation and exoskeletons has led to a diversity that is unrivalled amongst animals. However, because of the limited extensibility of exoskeleton chitin and cuticle components, they must be periodically shed and replaced with new larger ones, notably to accommodate the growing individuals encased within. Therefore, arthropods grow discontinuously by undergoing periodic moulting events, which follow a series of steps from the preparatory pre-moult phase to ecdysis itself and post-moult maturation of new exoskeletons. Each event represents a particularly vulnerable period in an arthropod's life cycle, so processes must be tightly regulated and meticulously executed to ensure successful transitions for normal growth and development. Decades of research in representative arthropods provide a foundation of understanding of the mechanisms involved. Building on this, studies continue to develop and test hypotheses on the presence and function of molecular components, including neuropeptides, hormones, and receptors, as well as the so-called early, late, and fate genes, across arthropod diversity. Here, we review the literature to develop a comprehensive overview of the status of accumulated knowledge of the genetic toolkit governing arthropod moulting. From biosynthesis and regulation of ecdysteroid and sesquiterpenoid hormones, to factors involved in hormonal stimulation responses and exoskeleton remodelling, we identify commonalities and differences, as well as highlighting major knowledge gaps, across arthropod groups. We examine the available evidence supporting current models of how components operate together to prepare for, execute, and recover from ecdysis, comparing reports from Chelicerata, Myriapoda, Crustacea, and Hexapoda. Evidence is generally highly taxonomically imbalanced, with most reports based on insect study systems. Biases are also evident in research on different moulting phases and processes, with the early triggers and late effectors generally being the least well explored. Our synthesis contrasts knowledge based on reported observations with reasonably plausible assumptions given current taxonomic sampling, and exposes weak assumptions or major gaps that need addressing. Encouragingly, advances in genomics are driving a diversification of tractable study systems by facilitating the cataloguing of putative genetic toolkits in previously under-explored taxa. Analysis of genome and transcriptome data supported by experimental investigations have validated the presence of an "ultra-conserved" core of arthropod genes involved in moulting processes. The molecular machinery has likely evolved with elaborations on this conserved pathway backbone, but more taxonomic exploration is needed to characterise lineage-specific changes and novelties. Furthermore, linking these to transformative innovations in moulting processes across Arthropoda remains hampered by knowledge gaps and hypotheses based on untested assumptions. Promisingly however, emerging from the synthesis is a framework that highlights research avenues from the underlying genetics to the dynamic molecular biology through to the complex physiology of moulting.
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Affiliation(s)
- Giulia Campli
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Olga Volovych
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Kenneth Kim
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Werner P Veldsman
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Harriet B Drage
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Idan Sheizaf
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Sinéad Lynch
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Ariel D Chipman
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Allison C Daley
- Institute of Earth Sciences, Quartier UNIL-Mouline, Bâtiment Géopolis, University of Lausanne, Lausanne, 1015, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Quartier UNIL-Sorge, Bâtiment Biophore, University of Lausanne, Lausanne, 1015, Switzerland
- SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Amphipôle, Lausanne, 1015, Switzerland
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3
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Wang D, Qiang Y, Guo J, Vannier J, Song Z, Peng J, Zhang B, Sun J, Yu Y, Zhang Y, Zhang T, Yang X, Han J. Early evolution of the ecdysozoan body plan. eLife 2024; 13:RP94709. [PMID: 38976315 PMCID: PMC11231812 DOI: 10.7554/elife.94709] [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] [Indexed: 07/09/2024] Open
Abstract
Extant ecdysozoans (moulting animals) are represented by a great variety of soft-bodied or articulated organisms that may or may not have appendages. However, controversies remain about the vermiform nature (i.e. elongated and tubular) of their ancestral body plan. We describe here Beretella spinosa gen. et sp. nov. a tiny (maximal length 3 mm) ecdysozoan from the lowermost Cambrian, Yanjiahe Formation, South China, characterized by an unusual sack-like appearance, single opening, and spiny ornament. Beretella spinosa gen. et sp. nov has no equivalent among animals, except Saccorhytus coronarius, also from the basal Cambrian. Phylogenetic analyses resolve both fossil species as a sister group (Saccorhytida) to all known Ecdysozoa, thus suggesting that ancestral ecdysozoans may have been non-vermiform animals. Saccorhytids are likely to represent an early off-shot along the stem-line Ecdysozoa. Although it became extinct during the Cambrian, this animal lineage provides precious insight into the early evolution of Ecdysozoa and the nature of the earliest representatives of the group.
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Affiliation(s)
- Deng Wang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
| | - Yaqin Qiang
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Junfeng Guo
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jean Vannier
- Université de Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Laboratoire de Géologie de Lyon: Terre, Planètes, Environnement (CNRS-UMR 5276), Villeurbanne, France
| | - Zuchen Song
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jiaxin Peng
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Boyao Zhang
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Jie Sun
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
- School of Earth Science and Resources, Key Laboratory of Western China's Mineral Resources and Geological Engineering, Ministry of Education, Chang'an University, Xi'an, China
| | - Yilun Yu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiheng Zhang
- School of Information Science and Technology, Northwest University, Xi'an, China
| | - Tao Zhang
- School of Information Science and Technology, Northwest University, Xi'an, China
| | - Xiaoguang Yang
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
| | - Jian Han
- State Key Laboratory of Continental Dynamics, Shaanxi Key Laboratory of Early Life & Environments and Department of Geology, Northwest University, Xi'an, China
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4
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Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mixed Wolbachia infections resolve rapidly during in vitro evolution. PLoS Pathog 2024; 20:e1012149. [PMID: 39052691 DOI: 10.1371/journal.ppat.1012149] [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: 03/25/2024] [Revised: 08/06/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between the two strains in cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.
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Affiliation(s)
- Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Pingting Wang
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Maximilian Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, United States of America
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, United States of America
| | - William T Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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5
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Gainett G, Klementz BC, Setton EVW, Simian C, Iuri HA, Edgecombe GD, Peretti AV, Sharma PP. A plurality of morphological characters need not equate with phylogenetic accuracy: A rare genomic change refutes the placement of Solifugae and Pseudoscorpiones in Haplocnemata. Evol Dev 2024; 26:e12467. [PMID: 38124251 DOI: 10.1111/ede.12467] [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: 08/30/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Recent advances in higher-level invertebrate phylogeny have leveraged shared features of genomic architecture to resolve contentious nodes across the tree of life. Yet, the interordinal relationships within Chelicerata have remained recalcitrant given competing topologies in recent molecular analyses. As such, relationships between topologically unstable orders remain supported primarily by morphological cladistic analyses. Solifugae, one such unstable chelicerate order, has long been thought to be the sister group of Pseudoscorpiones, forming the clade Haplocnemata, on the basis of eight putative morphological synapomorphies. The discovery, however, of a shared whole genome duplication placing Pseudoscorpiones in Arachnopulmonata provides the opportunity for a simple litmus test evaluating the validity of Haplocnemata. Here, we present the first developmental transcriptome of a solifuge (Titanopuga salinarum) and survey copy numbers of the homeobox genes for evidence of systemic duplication. We find that over 70% of the identified homeobox genes in T. salinarum are retained in a single copy, while representatives of the arachnopulmonates retain orthologs of those genes as two or more copies. Our results refute the placement of Solifugae in Haplocnemata. Subsequent reevaluation of putative interordinal morphological synapomorphies among chelicerates reveals a high incidence of homoplasy, reversals, and inaccurate coding within Haplocnemata and other small clades, as well as Arachnida more broadly, suggesting existing morphological character matrices are insufficient to resolve chelicerate phylogeny.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin C Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emily V W Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Catalina Simian
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Hernán A Iuri
- División de Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Gregory D Edgecombe
- Department of Earth Sciences, Division ES Invertebrates and Plants Palaeobiology, The Natural History Museum, London, UK
| | - Alfredo V Peretti
- Departamento de Diversidad Biológica y Ecología, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
- Laboratorio de Biología Reproductiva y Evolución, Consejo Nacional de Investigaciones Científicas Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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6
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Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M, Vellutini BC, Larsson T, Savage EL, Lopez MO, Hercog R, Provaznik J, Ordoñez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Özpolat BD, Arendt D. A genome resource for the marine annelid Platynereis dumerilii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600153. [PMID: 38948846 PMCID: PMC11213123 DOI: 10.1101/2024.06.21.600153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. dumerilii and of the closely related P. massiliensis and P. megalops, to facilitate comparative genomic approaches and help explore Platynereis biology. We used long-read sequencing technology and chromosomal-conformation capture along with extensive transcriptomic resources to obtain and annotate a draft genome assembly of ~1.47 Gbp for P. dumerilii, of which more than half represent repeat elements. We predict around 29,000 protein-coding genes, with relatively large intron sizes, over 38,000 non-coding genes, and 580 miRNA loci. We further explore the high genetic variation (~3% heterozygosity) within the Platynereis species complex. Gene ontology reveals the most variable loci to be associated with pigmentation, development and immunity. The current work sets the stage for further development of Platynereis genomic resources.
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Affiliation(s)
- Kevin Nzumbi Mutemi
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Austria
| | - Leslie Pan
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Luca Santangeli
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Ryan W. Null
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Mette Handberg-Thorsager
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | | | - Tomas Larsson
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. Current: Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Emily L. Savage
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Current: Centre for Organismal Studies, University of Heidelberg, Heidelberg
| | - Mireia Osuna Lopez
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rajna Hercog
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany - not at EMBL anymore, do not know current address
| | - Jan Provaznik
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Diana Ordoñez-Rueda
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nayara Azevedo
- European Molecular Biology Laboratory, Genomics Core Facility, Meyerhofstrasse 1, 69117 Heidelberg, Germany. - not at EMBL anymore, do not know current address
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France. - deceased
| | - Pavel Tomancak
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Vladimir Benes
- EMBL, Genomics Core Facility, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong
| | - Conrad Helm
- Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - B. Duygu Özpolat
- Current: Department of Biology, Washington University in Saint Louis, MO, USA 63139 Previous: Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA. 02543. USA
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Centre for Organismal Studies (COS) University of Heidelberg, 69120 Heidelberg, Germany
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7
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Shook EN, Barlow GT, Garcia-Rosales D, Gibbons CJ, Montague TG. Dynamic skin behaviors in cephalopods. Curr Opin Neurobiol 2024; 86:102876. [PMID: 38652980 DOI: 10.1016/j.conb.2024.102876] [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: 11/01/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/25/2024]
Abstract
The coleoid cephalopods (cuttlefish, octopus, and squid) are a group of soft-bodied mollusks that exhibit a wealth of complex behaviors, including dynamic camouflage, object mimicry, skin-based visual communication, and dynamic body patterns during sleep. Many of these behaviors are visually driven and engage the animals' color changing skin, a pixelated display that is directly controlled by neurons projecting from the brain. Thus, cephalopod skin provides a direct readout of neural activity in the brain. During camouflage, cephalopods recreate on their skin an approximation of what they see, providing a window into perceptual processes in the brain. Additionally, cephalopods communicate their internal state during social encounters using innate skin patterns, and create waves of pigmentation on their skin during periods of arousal. Thus, by leveraging the visual displays of cephalopods, we can gain insight into how the external world is represented in the brain and how this representation is transformed into a recapitulation of the world on the skin. Here, we describe the rich skin behaviors of the coleoid cephalopods, what is known about cephalopod neuroanatomy, and how advancements in gene editing, machine learning, optical imaging, and electrophysiological tools may provide an opportunity to explore the neural bases of these fascinating behaviors.
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Affiliation(s)
- Erica N Shook
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - George Thomas Barlow
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Daniella Garcia-Rosales
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Connor J Gibbons
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Tessa G Montague
- The Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
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8
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Mirchandani C, Wang P, Jacobs J, Genetti M, Pepper-Tunick E, Sullivan WT, Corbett-Detig R, Russell SL. Mixed Wolbachia infections resolve rapidly during in vitro evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586911. [PMID: 38585949 PMCID: PMC10996604 DOI: 10.1101/2024.03.27.586911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The intracellular symbiont Wolbachia pipientis evolved after the divergence of arthropods and nematodes, but it reached high prevalence in many of these taxa through its abilities to infect new hosts and their germlines. Some strains exhibit long-term patterns of co-evolution with their hosts, while other strains are capable of switching hosts. This makes strain selection an important factor in symbiont-based biological control. However, little is known about the ecological and evolutionary interactions that occur when a promiscuous strain colonizes an infected host. Here, we study what occurs when two strains come into contact in host cells following horizontal transmission and infection. We focus on the faithful wMel strain from Drosophila melanogaster and the promiscuous wRi strain from Drosophila simulans using an in vitro cell culture system with multiple host cell types and combinatorial infection states. Mixing D. melanogaster cell lines stably infected with wMel and wRi revealed that wMel outcompetes wRi quickly and reproducibly. Furthermore, wMel was able to competitively exclude wRi even from minuscule starting quantities, indicating that this is a nearly deterministic outcome, independent of the starting infection frequency. This competitive advantage was not exclusive to wMel's native D. melanogaster cell background, as wMel also outgrew wRi in D. simulans cells. Overall, wRi is less adept at in vitro growth and survival than wMel and its in vivo state, revealing differences between cellular and humoral regulation. These attributes may underlie the observed low rate of mixed infections in nature and the relatively rare rate of host-switching in most strains. Our in vitro experimental framework for estimating cellular growth dynamics of Wolbachia strains in different host species, tissues, and cell types provides the first strategy for parameterizing endosymbiont and host cell biology at high resolution. This toolset will be crucial to our application of these bacteria as biological control agents in novel hosts and ecosystems.
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Affiliation(s)
- Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Pingting Wang
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Jodie Jacobs
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Maximilian Genetti
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, USA
| | - William T Sullivan
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Shelbi L Russell
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, United States
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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9
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Guan G, Luo C, Tang LH, Tang C. Modulating cell proliferation by asymmetric division: A conserved pattern in the early embryogenesis of nematode species. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001006. [PMID: 38505394 PMCID: PMC10949086 DOI: 10.17912/micropub.biology.001006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/24/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
Abstract
In the early stage of the nematode Caenorhabditis elegans embryogenesis, the zygote divides asymmetrically into a symmetric fast lineage and an asymmetric slow lineage, producing 16 and 8 cells respectively almost at the same time, followed by the onset of gastrulation. It was recently reported that this cell division pattern is optimal for rapid cell proliferation. In this work, we compare the cell lineages of 9 nematode species, revealing that this pattern is conserved for >60 million years. It further suggests that such lineage design has an important functional role and it might speed up embryonic development in the nematode kingdom, not limited to C. elegans , and independent of the maternal-zygotic transition dynamics.
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Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Current Address: Department of Systems Biology, Harvard Medical School
- Current Address: Department of Data Science, Dana-Farber Cancer Institute
| | - Ce Luo
- Center for Quantitative Biology, Peking University
| | - Lei-Han Tang
- South Bay Interdisciplinary Science Center, Songshan Lake Materials Laboratory
- Department of Physics, Hong Kong Baptist University
- Institute of Computational and Theoretical Studies, Hong Kong Baptist University
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University
| | - Chao Tang
- Center for Quantitative Biology, Peking University
- Peking-Tsinghua Center for Life Sciences, Peking University
- School of Physics, Peking University
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10
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Pandey T, Kalluraya CA, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. Acquired stress resilience through bacteria-to-nematode interdomain horizontal gene transfer. EMBO J 2023; 42:e114835. [PMID: 37953666 PMCID: PMC10711659 DOI: 10.15252/embj.2023114835] [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: 06/24/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 11/14/2023] Open
Abstract
Natural selection drives the acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisitions in immunity, metabolic, and reproduction function via interdomain HGT (iHGT) from bacteria. Here, we report that the nematode gene rml-3 has been acquired by iHGT from bacteria and that it enables exoskeleton resilience and protection against environmental toxins in Caenorhabditis elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most similar to bacterial enzymes that biosynthesize L-rhamnose, a cell-wall polysaccharide component. C. elegans rml-3 is highly expressed during larval development and upregulated in developing seam cells upon heat stress and during the stress-resistant dauer stage. rml-3 deficiency impairs cuticle integrity, barrier functions, and nematode stress resilience, phenotypes that can be rescued by exogenous L-rhamnose. We propose that interdomain HGT of an ancient bacterial rml-3 homolog has enabled L-rhamnose biosynthesis in nematodes, facilitating cuticle integrity and organismal resilience to environmental stressors during evolution. These findings highlight a remarkable contribution of iHGT on metazoan evolution conferred by the domestication of a bacterial gene.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
| | | | - Bingying Wang
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
| | - Ting Xu
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Xinya Huang
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | - Shouhong Guang
- Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui ProvinceUniversity of Science and Technology of ChinaHefeiChina
| | | | - Dengke K Ma
- Cardiovascular Research Institute and Department of PhysiologyUniversity of California San FranciscoSan FranciscoCAUSA
- Innovative Genomics InstituteUniversity of CaliforniaBerkeleyCAUSA
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11
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Zhang H, Xiao S, Eriksson ME, Duan B, Maas A. Musculature of an Early Cambrian cycloneuralian animal. Proc Biol Sci 2023; 290:20231803. [PMID: 37817588 PMCID: PMC10565385 DOI: 10.1098/rspb.2023.1803] [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: 08/10/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023] Open
Abstract
Cycloneuralians are ecdysozoans with a fossil record extending to the Early Cambrian Fortunian Age and represented mostly by cuticular integuments. However, internal anatomies of Fortunian cycloneuralians are virtually unknown, hampering our understanding of their functional morphology and phylogenetic relationships. Here we report the exceptional preservation of cycloneuralian introvert musculature in Fortunian rocks of South China. The musculature consists of an introvert body-wall muscular grid of four circular and 36 radially arranged longitudinal muscle bundles, as well as an introvert circular muscle associated with 19 roughly radially arranged, short retractors. Collectively, these features support at least a scalidophoran affinity, and the absence of muscles associated with a mouth cone and scalids further indicates a priapulan affinity. As in modern scalidophorans, the fossil musculature, and particularly the introvert circular muscle retractors, may have controlled introvert inversion and facilitated locomotion and feeding. This work supports the evolution of scalidophoran-like or priapulan-like introvert musculature in cycloneuralians at the beginning of the Cambrian Period.
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Affiliation(s)
- Huaqiao Zhang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China
| | - Shuhai Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Baichuan Duan
- Key Laboratory of Marine Geology and Metallogeny, First Institute of Oceanography, Ministry of Natural Resource, Qingdao 266061, People's Republic of China
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12
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Li G, Wilschut RA, Luo S, Chen H, Wang X, Du G, Geisen S. Nematode biomass changes along an elevational gradient are trophic group dependent but independent of body size. GLOBAL CHANGE BIOLOGY 2023; 29:4898-4909. [PMID: 37337363 DOI: 10.1111/gcb.16814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023]
Abstract
Aboveground, large and higher trophic-level organisms often respond more strongly to environmental changes than small and lower trophic-level organisms. However, whether this trophic or size-dependent sensitivity also applies to the most abundant animals, microscopic soil-borne nematodes, remains largely unknown. Here, we sampled an altitudinal transect across the Tibetan Plateau and applied a community-weighted mean (CWM) approach to test how differences in climatic and edaphic properties affect nematode CWM biomass at the level of community, trophic group and taxon mean biomass within trophic groups. We found that climatic and edaphic properties, particularly soil water-related properties, positively affected nematode CWM biomass, with no overall impact of altitude on nematode CWM biomass. Higher trophic-level omnivorous and predatory nematodes responded more strongly to climatic and edaphic properties, particularly to temperature, soil pH, and soil water content than lower trophic-level bacterivorous and fungivorous nematodes. However, these differences were likely not (only) driven by size, as we did not observe significant interactions between climatic and edaphic properties and mean biomasses within trophic groups. Together, our research implies a stronger, size-independent trophic sensitivity of higher trophic-level nematodes compared with lower trophic-level ones. Therefore, our findings provide new insights into the mechanisms underlying nematode body size structure in alpine grasslands and highlight that traits independent of size need to be found to explain increased sensitivity of higher trophic-level nematodes to climatic and edaphic properties, which might affect soil functioning.
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Affiliation(s)
- Guixin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Shuaiwei Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Han Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiangtai Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Guozhen Du
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, Gansu, China
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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13
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Pandey T, Kalluraya C, Wang B, Xu T, Huang X, Guang S, Daugherty MD, Ma DK. Acquired stress resilience through bacteria-to-nematode horizontal gene transfer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.20.554039. [PMID: 37662235 PMCID: PMC10473587 DOI: 10.1101/2023.08.20.554039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Natural selection drives acquisition of organismal resilience traits to protect against adverse environments. Horizontal gene transfer (HGT) is an important evolutionary mechanism for the acquisition of novel traits, including metazoan acquisition of functions in immunity, metabolism, and reproduction via interdomain HGT (iHGT) from bacteria. We report that the nematode gene rml-3, which was acquired by iHGT from bacteria, enables exoskeleton resilience and protection against environmental toxins in C. elegans. Phylogenetic analysis reveals that diverse nematode RML-3 proteins form a single monophyletic clade most highly similar to bacterial enzymes that biosynthesize L-rhamnose to build cell wall polysaccharides. C. elegans rml-3 is regulated in developing seam cells by heat stress and stress-resistant dauer stage. Importantly, rml-3 deficiency impairs cuticle integrity, barrier functions and organismal stress resilience, phenotypes that are rescued by exogenous L-rhamnose. We propose that iHGT of an ancient bacterial rml-3 homolog enables L-rhamnose biosynthesis in nematodes that facilitates cuticle integrity and organismal resilience in adaptation to environmental stresses during evolution. These findings highlight the remarkable contribution of iHGT on metazoan evolution that is conferred by the domestication of bacterial genes.
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Affiliation(s)
- Taruna Pandey
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Chinmay Kalluraya
- Department of Molecular Biology, University of California, San Diego, San Diego, USA
| | - Bingying Wang
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
| | - Ting Xu
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Xinya Huang
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Shouhong Guang
- The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, San Diego, USA
| | - Dengke K. Ma
- Cardiovascular Research Institute and Department of Physiology, University of California San Francisco, San Francisco, USA
- Innovative Genomics Institute, University of California, Berkeley, USA
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14
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Bernot JP, Owen CL, Wolfe JM, Meland K, Olesen J, Crandall KA. Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling. Mol Biol Evol 2023; 40:msad175. [PMID: 37552897 PMCID: PMC10414812 DOI: 10.1093/molbev/msad175] [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: 10/30/2022] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 08/10/2023] Open
Abstract
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.
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Affiliation(s)
- James P Bernot
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, ℅ National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth Meland
- Department of Biology, University of Bergen, Bergen, Norway
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Keith A Crandall
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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15
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Zhang P, Yang Y, Xu Y, Cui Z. Analyses of the Dmrt family in a decapod crab, Eriocheir sinensis uncover new facets on the evolution of DM domain genes. Front Physiol 2023; 14:1201846. [PMID: 37304820 PMCID: PMC10252143 DOI: 10.3389/fphys.2023.1201846] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
DM domain genes are a group of transcription factors that are integral to sexual development and its evolution in metazoans. Their functions and regulatory mechanisms are not well understood in Malacostraca (crabs and crayfish) while these sex regulators have been widely identified in the past decade. In this study, the Dmrt family was investigated in the decapod crab, Eriocheir sinensis. We find that most members of the EsDmrt family begin to enrich around the juvenile 1 stage. In reproductive organs, EsDsx1, EsDsx2, EsiDMY and EsiDmrt1a highly express in the male-specific androgenic gland (AG), while EsDmrt-like, EsDsx-like, EsDmrt11E, and EsiDmrt1b show relatively high expression in testis. Also, we find the highly aberrant expression of EsiDMY and EsiDmrt1a in the chimeric AG, strongly indicating their function in AG development. Moreover, RNA interference of EsDsx1, EsiDMY, and EsiDmrt1a results in a significant decrease in transcription of the Insulin-like androgenic hormone (IAG), respectively. Our findings suggest that Dmrt genes in E. sinensis primarily function in male sexual differentiation, especially in AG development. Besides, this study identifies two unique groups of Dmrt genes in Malacostraca: Dsx and iDmrt1. In Malacostraca Dsx, we uncover a cryptic mutation in the eight zinc motif-specific residues, which were firmly believed to be invariant across the Dmrt family. This mutation sets the Malacostraca Dsx apart from all the other Dmrt genes and implies a different way of transcriptional regulation. Genes from the iDmrt1 group show phylogenetical limitation to the malacostracan species and underwent positive selection, suggesting their highly specialized gene function to this class. Based on these findings, we propose that Dsx and iDmrt1 in Malacostraca have developed unique transcriptional regulation mechanisms to facilitate AG development. We hope that this study would contribute to our understandings of sexual development in Malacostraca and provide new insights into the evolutionary history of the Dmrt family.
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Affiliation(s)
- Peng Zhang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yanan Yang
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yuanfeng Xu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo, China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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16
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Jahn H, Hammel JU, Göpel T, Wirkner CS, Mayer G. A multiscale approach reveals elaborate circulatory system and intermittent heartbeat in velvet worms (Onychophora). Commun Biol 2023; 6:468. [PMID: 37117786 PMCID: PMC10147947 DOI: 10.1038/s42003-023-04797-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 04/03/2023] [Indexed: 04/30/2023] Open
Abstract
An antagonistic hemolymph-muscular system is essential for soft-bodied invertebrates. Many ecdysozoans (molting animals) possess neither a heart nor a vascular or circulatory system, whereas most arthropods exhibit a well-developed circulatory system. How did this system evolve and how was it subsequently modified in panarthropod lineages? As the closest relatives of arthropods and tardigrades, onychophorans (velvet worms) represent a key group for addressing this question. We therefore analyzed the entire circulatory system of the peripatopsid Euperipatoides rowelli and discovered a surprisingly elaborate organization. Our findings suggest that the last common ancestor of Onychophora and Arthropoda most likely possessed an open vascular system, a posteriorly closed heart with segmental ostia, a pericardial sinus filled with nephrocytes and an impermeable pericardial septum, whereas the evolutionary origin of plical and pericardial channels is unclear. Our study further revealed an intermittent heartbeat-regular breaks of rhythmic, peristaltic contractions of the heart-in velvet worms, which might stimulate similar investigations in arthropods.
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Affiliation(s)
- Henry Jahn
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, D-34132, Kassel, Germany.
| | - Jörg U Hammel
- Institute of Materials Physics, Helmholtz-Zentrum Hereon at DESY, Notkestraße 85, D-22607, Hamburg, Germany
| | - Torben Göpel
- Multiscale Biology, Johann-Friedrich-Blumenbach Institut für Zoologie und Anthropologie, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, D-37077, Göttingen, Germany
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA
| | - Christian S Wirkner
- Institut für Allgemeine und Spezielle Zoologie, Institut für Biowissenschaften, Universität Rostock, Universitätsplatz 2, D-18055, Rostock, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Straße 40, D-34132, Kassel, Germany
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17
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Novotná Floriančičová K, Baltzis A, Smejkal J, Czerneková M, Kaczmarek Ł, Malý J, Notredame C, Vinopal S. Phylogenetic and functional characterization of water bears (Tardigrada) tubulins. Sci Rep 2023; 13:5194. [PMID: 36997657 PMCID: PMC10063605 DOI: 10.1038/s41598-023-31992-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
Tardigrades are microscopic ecdysozoans that can withstand extreme environmental conditions. Several tardigrade species undergo reversible morphological transformations and enter into cryptobiosis, which helps them to survive periods of unfavorable environmental conditions. However, the underlying molecular mechanisms of cryptobiosis are mostly unknown. Tubulins are evolutionarily conserved components of the microtubule cytoskeleton that are crucial in many cellular processes. We hypothesize that microtubules are necessary for the morphological changes associated with successful cryptobiosis. The molecular composition of the microtubule cytoskeleton in tardigrades is unknown. Therefore, we analyzed and characterized tardigrade tubulins and identified 79 tardigrade tubulin sequences in eight taxa. We found three α-, seven β-, one γ-, and one ε-tubulin isoform. To verify in silico identified tardigrade tubulins, we also isolated and sequenced nine out of ten predicted Hypsibius exemplaris tubulins. All tardigrade tubulins were localized as expected when overexpressed in mammalian cultured cells: to the microtubules or to the centrosomes. The presence of a functional ε-tubulin, clearly localized to centrioles, is attractive from a phylogenetic point of view. Although the phylogenetically close Nematoda lost their δ- and ε-tubulins, some groups of Arthropoda still possess them. Thus, our data support the current placement of tardigrades into the Panarthropoda clade.
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Affiliation(s)
- Kamila Novotná Floriančičová
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | | | - Jiří Smejkal
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Michaela Czerneková
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Jan Malý
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic
| | - Cedric Notredame
- Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stanislav Vinopal
- Department of Biology, Faculty of Science, J. E. Purkyně University (UJEP), Usti Nad Labem, Czech Republic.
- Centre for Nanotechnology and Biotechnology, Faculty of Science, UJEP, Usti Nad Labem, Czech Republic.
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18
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Laursen WJ, Budelli G, Tang R, Chang EC, Busby R, Shankar S, Gerber R, Greppi C, Albuquerque R, Garrity PA. Humidity sensors that alert mosquitoes to nearby hosts and egg-laying sites. Neuron 2023; 111:874-887.e8. [PMID: 36640768 PMCID: PMC10023463 DOI: 10.1016/j.neuron.2022.12.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/23/2022] [Accepted: 12/19/2022] [Indexed: 01/15/2023]
Abstract
To reproduce and to transmit disease, female mosquitoes must obtain blood meals and locate appropriate sites for egg laying (oviposition). While distinct sensory cues drive each behavior, humidity contributes to both. Here, we identify the mosquito's humidity sensors (hygrosensors). Using generalizable approaches designed to simplify genetic analysis in non-traditional model organisms, we demonstrate that the ionotropic receptor Ir93a mediates mosquito hygrosensation as well as thermosensation. We further show that Ir93a-dependent sensors drive human host proximity detection and blood-feeding behavior, consistent with the overlapping short-range heat and humidity gradients these targets generate. After blood feeding, gravid females require Ir93a to seek high humidity associated with preferred egg-laying sites. Reliance on Ir93a-dependent sensors to promote blood feeding and locate potential oviposition sites is shared between the malaria vector Anopheles gambiae and arbovirus vector Aedes aegypti. These Ir93a-dependent systems represent potential targets for efforts to control these human disease vectors.
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Affiliation(s)
- Willem J Laursen
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Gonzalo Budelli
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Ruocong Tang
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Elaine C Chang
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Rachel Busby
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Shruti Shankar
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Rachel Gerber
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Chloe Greppi
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Rebecca Albuquerque
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | - Paul A Garrity
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA.
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19
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Schachat SR, Goldstein PZ, Desalle R, Bobo DM, Boyce CK, Payne JL, Labandeira CC. Illusion of flight? Absence, evidence and the age of winged insects. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac137] [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
Abstract
The earliest fossils of winged insects (Pterygota) are mid-Carboniferous (latest Mississippian, 328–324 Mya), but estimates of their age based on fossil-calibrated molecular phylogenetic studies place their origin at 440–370 Mya during the Silurian or Devonian. This discrepancy would require that winged insects evaded fossilization for at least the first ~50 Myr of their history. Here, we examine the plausibility of such a gap in the fossil record, and possible explanations for it, based on comparisons with the fossil records of other arthropod groups, the distribution of first occurrence dates of pterygote families, phylogenetically informed simulations of the fossilization of Palaeozoic insects, and re-analysis of data presented by Misof and colleagues using updated fossil calibrations under a variety of prior probability settings. We do not find support for the mechanisms previously suggested to account for such an extended gap in the pterygote fossil record, including sampling bias, preservation bias, and body size. We suggest that inference of an early origin of Pterygota long prior to their first appearance in the fossil record is probably an analytical artefact of taxon sampling and choice of fossil calibration points, possibly compounded by heterogeneity in rates of sequence evolution or speciation, including radiations or ‘bursts’ during their early history.
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Affiliation(s)
- Sandra R Schachat
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Paul Z Goldstein
- Systematic Entomology Laboratory, USDA, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
| | - Rob Desalle
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
| | - Dean M Bobo
- American Museum of Natural History, Sackler Institute for Comparative Genomics , New York, NY , USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University , New York, NY , USA
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Jonathan L Payne
- Department of Geological Sciences, Stanford University , Stanford, CA , USA
| | - Conrad C Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution , Washington, DC , USA
- Department of Entomology and Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park , MD , USA
- Capital Normal University, School of Life Sciences , Beijing , China
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20
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Pepato AR, Dos S Costa SG, Harvey MS, Klimov PB. One-way ticket to the blue: A large-scale, dated phylogeny revealed asymmetric land-to-water transitions in acariform mites (Acari: Acariformes). Mol Phylogenet Evol 2022; 177:107626. [PMID: 36096463 DOI: 10.1016/j.ympev.2022.107626] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/11/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022]
Abstract
Acariform mites are an ancient and megadiverse lineage that may have experienced a complex pattern of invasions into terrestrial and aquatic habitats. These among-realm transitions may relate to periods of turmoil in Earth's history or be simply results of uneven biodiversity patterns across habitats. Here, we inferred a dated, representative acariform phylogeny (five genes, 9,200 bp aligned, 367 terminals belonging to 150 ingroup plus 15 outgroup families, 23 fossil calibration points) which was used to infer transitions between marine/freshwater/terrestrial habitats. We detected four unambiguous transitions from terrestrial to freshwater habitats (Hydrozetes, Naiadacarus, Fusohericia, Afronothrus, Homocaligus); one from freshwater to marine (Pontarachnidae), and four from marine to brackish or freshwater transitions (all among Halacaridae: Acarothrix; Halacarellus petiti; Copidognathus sp.; clade Limnohalacarus + Soldanellonyx + Porohalacarus + Porolohmannella). One transition to the sea was inferred ambiguously with respect to the ancestor being either terrestrial or freshwater (Hyadesiidae), and another must be most carefully examined by adding potential related taxa (Selenoribatidae + Fortuyniidae). Finally, we inferred a single, remarkable transition from aquatic to terrestrial habitats involving early evolution of the large and ecologically diverse lineage: the ancestor of the Halacaridae + Parasitengona clade was probably freshwater given our dataset, thus making terrestrial Parasitengona secondarily terrestrial. Overall, our results suggested a strong asymmetry in environmental transitions: the majority occurred from terrestrial to aquatic habitats. This asymmetry is probably linked to mites' biological properties and uneven biodiversity patterns across habitats rather than Earth's geological history. Since the land holds more acariform diversity than water habitats, a shift from the former is more likely than from the latter. We inferred the following relationships: alicid endeostigmatid + eriophyoid (Alycidae, (Nanorchestidae, (Nematalycidae, Eriophyoidea))) being sister group to the remaining Acariformes: (proteonematalycid Endeostigmata, alicorhagiid Endeostigmata, Trombidiformes, Oribatida (including Astigmata)). Trombidiform relationships had several novel rearrangements: (i) traditional Eupodina lacked support for the inclusion of Bdelloidea; (ii) Teneriffidae, traditionally placed among Anystina, was consistently recovered in a clade including Heterostigmata in Eleutherengona; (iii) several lineages, such as Adamystidae, Paratydeidae, Caeculidae and Erythracaridae, were recovered in a large clade along other Anystina and Eleutherengona, suggesting single origins of several fundamental character states, such as the reduction of the cheliceral fixed digit and development of the palpal thumb-claw complex.
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Affiliation(s)
- Almir R Pepato
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Zoologia, Laboratório de Sistemática e Evolução de Ácaros Acariformes, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte - MG ZIP: 31270-901, Brazil; Tyumen State University, X-BIO Institute, 10 Semakova Str., 625003 Tyumen, Russia.
| | - Samuel G Dos S Costa
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Zoologia, Laboratório de Sistemática e Evolução de Ácaros Acariformes, Av. Antonio Carlos, 6627, Pampulha, Belo Horizonte - MG ZIP: 31270-901, Brazil
| | - Mark S Harvey
- Collections & Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia; School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Pavel B Klimov
- Purdue University, Lilly Hall of Life Sciences, G-226, 915 W State St, West Lafayette, IN 47907, United States; Tyumen State University, X-BIO Institute, 10 Semakova Str., 625003 Tyumen, Russia
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21
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Inui N, Kimbara R, Yamaguchi H, Miura T. Pleopodal lung development in a terrestrial isopod, Porcellio scaber (Oniscidea). ARTHROPOD STRUCTURE & DEVELOPMENT 2022; 71:101210. [PMID: 36206666 DOI: 10.1016/j.asd.2022.101210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/24/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
During evolution, various lineages of arthropods colonized land and independently acquired air-breathing organs. Some taxa of oniscidean isopods (Crustacea, Isopoda, Oniscidea) are the most successful crustacean lineages on land and possess organs called "lungs" or "pseudotrachea" for air-breathing in their abdominal appendages, i.e., in pleopods. Although these lungs are important for adapting to the terrestrial environment, their developmental process has not yet been elucidated. In the present study, we investigated the process of lung development in Porcellio scaber, the common rough woodlouse with pleopodal lungs in the first two pairs of pleopods. The lungs in the second pleopods developed at the manca 1 stage (immediately after hatching) and became functional at the manca 2 stage. In the first pleopods, which appear at the manca 3 stage, the lungs were gradually developed during the manca 3 stage and became functional in post-manca juveniles. In the second pleopods, epithelial invaginations led to lung development. These results suggest that some novel developmental mechanisms with epithelial invaginations and cuticle formation were acquired during terrestrialization, resulting in the development of functional lungs in the terrestrial isopod lineages.
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Affiliation(s)
- Naoto Inui
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Ryosuke Kimbara
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Haruka Yamaguchi
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan
| | - Toru Miura
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Misaki, Miura, Kanagawa, 238-0225, Japan.
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22
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Tchesunov AV, Nikolaeva OV, Rusin LY, Sanamyan NP, Panina EG, Miljutin DM, Gorelysheva DI, Pegova AN, Khromova MR, Mardashova MV, Mikhailov KV, Yushin VV, Petrov NB, Lyubetsky VA, Nikitin MA, Aleoshin VV. Paraphyly of Marimermithida refines primary routes of transition to parasitism in roundworms. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac070] [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
Parasitic life-strategies in the phylum Nematoda (roundworms) are remarkably diverse and intricate in terms of evolution and taxonomy. By analysing novel rDNA data obtained on rare host-associated groups with unusual biology, we reveal paraphyly of the last major taxon with uncertain higher-rank classification that united solely parasitic nematodes (Marimermithida) to show that primarily marine parasitism only emerged independently and repeatedly in a few free-living lineages. We report secondary seaward ingression of land-based parasites (Mermithida) via invading hosts in the subtidal zone to illustrate the host-borne scenario of oceanic fish and mammal colonization by primarily terrestrial parasites (Spiruria). We also present the first molecular data on marine nematodes from unicellular hosts (foraminiferan protozoans) to demonstrate the independent origins of exploitative nematode associations at a microscopic scale. We argue that, in contrast with primarily intestinal associations arising from saprotrophy and commensalism, non-intestinal host capture (colonization of host body cavity or internal organs) is likely to be a primary route of transition to truly exploitative parasitism in roundworms. Predispositions to host capture in nematode morphology, ecology and life cycles imply its evolution as part of innate pre-adaptations to crossing environmental boundaries to enable multiple successful transitions to parasitism in the phylum history.
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Affiliation(s)
- Alexei V Tchesunov
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Olga V Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Leonid Yu Rusin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Nadezda P Sanamyan
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | - Elena G Panina
- Kamchatka Branch of Pacific Geographical Institute, Far Eastern Branch of the Russian Academy of Sciences , Petropavlovsk-Kamchatsky , Russia
| | | | - Daria I Gorelysheva
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences , Moscow , Russia
| | - Anna N Pegova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria R Khromova
- Faculty of Biology, Lomonosov Moscow State University , Moscow , Russian Federation
| | - Maria V Mardashova
- Marine Research Center, Lomonosov Moscow State University , Moscow , Russia
| | - Kirill V Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Yushin
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences , Vladivostok , Russia
| | - Nikolai B Petrov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Mikhail A Nikitin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
| | - Vladimir V Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University , Moscow , Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences , Moscow , Russia
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23
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He S, Jiang B, Chakraborty A, Yu G. The Evolution of Glycoside Hydrolase Family 1 in Insects Related to Their Adaptation to Plant Utilization. INSECTS 2022; 13:786. [PMID: 36135486 PMCID: PMC9500737 DOI: 10.3390/insects13090786] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Insects closely interact with plants with multiple genes involved in their interactions. β-glucosidase, constituted mainly by glycoside hydrolase family 1 (GH1), is a crucial enzyme in insects to digest plant cell walls and defend against natural enemies with sequestered plant metabolites. To gain more insights into the role of this enzyme in plant-insect interactions, we analyzed the evolutionary history of the GH1 gene family with publicly available insect genomes. We found that GH1 is widely present in insects, while the gene numbers are significantly higher in insect herbivores directly feeding on plant cell walls than in other insects. After reconciling the insect GH1 gene tree with a species tree, we found that the patterns of duplication and loss of GH1 genes differ among insect orders, which may be associated with the evolution of their ecology. Furthermore, the majority of insects' GH1 genes were tandem-duplicated and subsequently went through neofunctionalization. This study shows the evolutionary history of an important gene family GH1 in insects and facilitates our understanding of the evolution of insect-plant interactions.
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Affiliation(s)
- Shulin He
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Bin Jiang
- College of Life Science, Anhui Normal University, Beijing Rd. 1, Wuhu 241000, China
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Guozhi Yu
- College of Life Science, Sichuan Agricultural University, Xinkang Rd. 46, Ya’an 625014, China
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24
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Functional importance of the mandibular skeleto-muscular system in the bivalved arthropod Heterocypris incongruens (Crustacea, Ostracoda, Cyprididae). Naturwissenschaften 2022; 109:37. [DOI: 10.1007/s00114-022-01806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/09/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022]
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25
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Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms. Nat Commun 2022; 13:3239. [PMID: 35688815 PMCID: PMC9187692 DOI: 10.1038/s41467-022-30578-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/06/2022] [Indexed: 12/02/2022] Open
Abstract
Many species with separate male and female individuals (termed ‘gonochorism’ in animals) have sex-linked genome regions. Here, we investigate evolutionary changes when genome regions become completely sex-linked, by analyses of multiple species of flatworms (Platyhelminthes; among which schistosomes recently evolved gonochorism from ancestral hermaphroditism), and roundworms (Nematoda) which have undergone independent translocations of different autosomes. Although neither the evolution of gonochorism nor translocations fusing ancestrally autosomal regions to sex chromosomes causes inevitable loss of recombination, we document that formerly recombining regions show genomic signatures of recombination suppression in both taxa, and become strongly genetically degenerated, with a loss of most genes. Comparisons with hermaphroditic flatworm transcriptomes show masculinisation and some defeminisation in schistosome gonad gene expression. We also find evidence that evolution of sex-linkage in nematodes is accompanied by transcriptional changes and dosage compensation. Our analyses also identify sex-linked genes that could assist future research aimed at controlling some of these important parasites. Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
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26
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Buatois LA, Davies NS, Gibling MR, Krapovickas V, Labandeira CC, MacNaughton RB, Mángano MG, Minter NJ, Shillito AP. The Invasion of the Land in Deep Time: Integrating Paleozoic Records of Paleobiology, Ichnology, Sedimentology, and Geomorphology. Integr Comp Biol 2022; 62:297-331. [PMID: 35640908 DOI: 10.1093/icb/icac059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/19/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
The invasion of the land was a complex, protracted process, punctuated by mass extinctions, that involved multiple routes from marine environments. We integrate paleobiology, ichnology, sedimentology, and geomorphology to reconstruct Paleozoic terrestrialization. Cambrian landscapes were dominated by laterally mobile rivers with unstable banks in the absence of significant vegetation. Temporary incursions by arthropods and worm-like organisms into coastal environments apparently did not result in establishment of continental communities. Contemporaneous lacustrine faunas may have been inhibited by limited nutrient delivery and high sediment loads. The Ordovician appearance of early land plants triggered a shift in the primary locus of the global clay mineral factory, increasing the amount of mudrock on the continents. The Silurian-Devonian rise of vascular land plants, including the first forests and extensive root systems, was instrumental in further retaining fine sediment on alluvial plains. These innovations led to increased architectural complexity of braided and meandering rivers. Landscape changes were synchronous with establishment of freshwater and terrestrial arthropod faunas in overbank areas, abandoned fluvial channels, lake margins, ephemeral lakes, and inland deserts. Silurian-Devonian lakes experienced improved nutrient availability, due to increased phosphate weathering and terrestrial humic matter. All these changes favoured frequent invasions to permament establishment of jawless and jawed fishes in freshwater habitats and the subsequent tetrapod colonization of the land. The Carboniferous saw rapid diversification of tetrapods, mostly linked to aquatic reproduction, and land plants, including gymnosperms. Deeper root systems promoted further riverbank stabilization, contributing to the rise of anabranching rivers and braided systems with vegetated islands. New lineages of aquatic insects developed and expanded novel feeding modes, including herbivory. Late Paleozoic soils commonly contain pervasive root and millipede traces. Lacustrine animal communities diversified, accompanied by increased food-web complexity and improved food delivery which may have favored permanent colonization of offshore and deep-water lake environments. These trends continued in the Permian, but progressive aridification favored formation of hypersaline lakes, which were stressful for colonization. The Capitanian and end-Permian extinctions affected lacustrine and fluvial biotas, particularly the invertebrate infauna, although burrowing may have allowed some tetrapods to survive associated global warming and increased aridification.
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Affiliation(s)
- Luis A Buatois
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Neil S Davies
- Department of Earth Sciences, University of Cambridge, Cambridge, Cambridgeshire CB2 3EQ, UK
| | - Martin R Gibling
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Verónica Krapovickas
- Departamento de Ciencias Geológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, C1428EGA, Argentina
| | - Conrad C Labandeira
- Department of Paleobiology, Smithsonian Institution, Washington DC 20013-7012, USA.,Department of Entomology and BEES Program, University of Maryland, College Park, Maryland 21740, USA.,College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Robert B MacNaughton
- Geological Survey of Canada (Calgary), Natural Resources Canada, Calgary, Alberta T2L 2A7, Canada
| | - M Gabriela Mángano
- Department of Geological Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Nicholas J Minter
- School of the Environment, Geography, and Geosciences, University of Portsmouth, Portsmouth, Hampshire PO1 3QL, UK
| | - Anthony P Shillito
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford, UK
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27
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Okamura B, Gruhl A, De Baets K. Evolutionary transitions of parasites between freshwater and marine environments. Integr Comp Biol 2022; 62:345-356. [PMID: 35604852 DOI: 10.1093/icb/icac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
Evolutionary transitions of organisms between environments have long fascinated biologists but attention has focused almost exclusively on free-living organisms and challenges to achieve such transitions. This bias requires addressing because parasites are a major component of biodiversity. We address this imbalance by focusing on transitions of parasitic animals between marine and freshwater environments. We highlight parasite traits and processes that may influence transition likelihood (e.g. transmission mode, life cycle, host use), and consider mechanisms and directions of transitions. Evidence for transitions in deep time and at present are described, and transitions in our changing world are considered. We propose that environmental transitions may be facilitated for endoparasites because hosts reduce exposure to physiologically challenging environments and argue that adoption of an endoparasitic lifestyle entails an equivalent transitioning process as organisms switch from living in one environment (e.g. freshwater, seawater, or air) to living symbiotically within hosts. Environmental transitions of parasites have repeatedly resulted in novel forms and diversification, contributing to the tree of life. Recognising the potential processes underlying present-day and future environmental transitions is crucial in view of our changing world and the current biodiversity crisis.
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Affiliation(s)
- Beth Okamura
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | | | - Kenneth De Baets
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
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28
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Weyandt N, Aghdam SA, Brown AMV. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. Front Microbiol 2022; 13:867392. [PMID: 35547116 PMCID: PMC9084900 DOI: 10.3389/fmicb.2022.867392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.
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Affiliation(s)
- Nicholas Weyandt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Shiva A Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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29
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Peng F, Engel U, Aliyu H, Rudat J. Origin and Evolution of Enzymes with MIO Prosthetic Group: Microbial Coevolution After the Mass Extinction Event. Front Genet 2022; 13:851738. [PMID: 35422843 PMCID: PMC9002059 DOI: 10.3389/fgene.2022.851738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/16/2022] [Indexed: 11/20/2022] Open
Abstract
After major mass extinction events, ancient plants and terrestrial vertebrates were faced with various challenges, especially ultraviolet (UV) light. These stresses probably resulted in changes in the biosynthetic pathways, which employed the MIO (3,5-dihydro-5-methylidene-4H-imidazole-4-one)-dependent enzymes (ammonia-lyase and aminomutase), leading to enhanced accumulation of metabolites for defense against UV radiation, pathogens, and microorganisms. Up to now, the origin and evolution of genes from this superfamily have not been extensively studied. In this report, we perform an analysis of the phylogenetic relations between the members of the aromatic amino acid MIO-dependent enzymes (AAM), which demonstrate that they most probably have a common evolutionary origin from ancient bacteria. In early soil environments, numerous bacterial species with tyrosine ammonia-lyase genes (TAL; EC 4.3.1.23) developed tyrosine aminomutase (TAM; EC 5.4.3.6) activity as a side reaction for competing with their neighbors in the community. These genes also evolved into other TAL-like enzymes, such as histidine ammonia-lyase (HAL, EC 4.3.1.3) and phenylalanine ammonia-lyase (PAL; EC 4.3.1.24), in different bacterial species for metabolite production and accumulation for adaptation to adverse terrestrial environmental conditions. On the other hand, the existence of phenylalanine aminomutase (PAM; EC 5.4.3.10) and phenylalanine/tyrosine ammonia-lyase (PTAL; EC 4.3.1.25) strongly indicates the horizontal gene transfer (HGT) between bacteria, fungi, and plants in symbiotic association after acquiring the PAL gene from their ancestor.
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Affiliation(s)
- Fei Peng
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ulrike Engel
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Habibu Aliyu
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Xie Y, Wang S, Wu S, Gao S, Meng Q, Wang C, Lan J, Luo L, Zhou X, Xu J, Gu X, He R, Yang Z, Peng X, Hu S, Yang G. Genome of the Giant Panda Roundworm Illuminates Its Host Shift and Parasitic Adaptation. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:366-381. [PMID: 34487863 PMCID: PMC9684166 DOI: 10.1016/j.gpb.2021.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/17/2021] [Accepted: 08/25/2021] [Indexed: 01/05/2023]
Abstract
Baylisascaris schroederi, a roundworm (ascaridoid) parasite specific to the bamboo-feeding giant panda (Ailuropoda melanoleuca), represents a leading cause of mortality in wild giant panda populations. Here, we present a 293-megabase chromosome-level genome assembly of B. schroederi to infer its biology, including host adaptations. Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations, suggesting their potential for transmission and rapid adaptation to new hosts. Genomic and anatomical lines of evidence, including expansion and positive selection of genes related to the cuticle and basal metabolisms, indicate that B. schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism. Additionally, we characterized the secretome of B. schroederi and predicted potential drug and vaccine targets for new control strategies. Overall, this genome resource provides new insights into the host adaptation of B. schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages. Our findings on the unique biology of B. schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Sen Wang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Shuangyang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17164, Sweden
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingshu Meng
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Chengdong Wang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Li Luo
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China; Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Xu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaobin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran He
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zijiang Yang
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD 20740, USA
| | - Xuerong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Chengdu 611130, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China.
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Han Z, Sieriebriennikov B, Susoy V, Lo WS, Igreja C, Dong C, Berasategui A, Witte H, Sommer RJ. Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes. Mol Biol Evol 2022; 39:msab370. [PMID: 34978575 PMCID: PMC8826503 DOI: 10.1093/molbev/msab370] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Horizontal gene transfer (HGT) enables the acquisition of novel traits via non-Mendelian inheritance of genetic material. HGT plays a prominent role in the evolution of prokaryotes, whereas in animals, HGT is rare and its functional significance is often uncertain. Here, we investigate horizontally acquired cellulase genes in the free-living nematode model organism Pristionchus pacificus. We show that these cellulase genes 1) are likely of eukaryotic origin, 2) are expressed, 3) have protein products that are secreted and functional, and 4) result in endo-cellulase activity. Using CRISPR/Cas9, we generated an octuple cellulase mutant, which lacks all eight cellulase genes and cellulase activity altogether. Nonetheless, this cellulase-null mutant is viable and therefore allows a detailed analysis of a gene family that was horizontally acquired. We show that the octuple cellulase mutant has associated fitness costs with reduced fecundity and slower developmental speed. Furthermore, by using various Escherichia coli K-12 strains as a model for cellulosic biofilms, we demonstrate that cellulases facilitate the procurement of nutrients from bacterial biofilms. Together, our analysis of cellulases in Pristionchus provides comprehensive evidence from biochemistry, genetics, and phylogeny, which supports the integration of horizontally acquired genes into the complex life history strategy of this soil nematode.
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Affiliation(s)
- Ziduan Han
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Vladislav Susoy
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Wen-Sui Lo
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Catia Igreja
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Chuanfu Dong
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | | | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology, Tuebingen, Germany
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Martin C, Jahn H, Klein M, Hammel JU, Stevenson PA, Homberg U, Mayer G. The velvet worm brain unveils homologies and evolutionary novelties across panarthropods. BMC Biol 2022; 20:26. [PMID: 35073910 PMCID: PMC9136957 DOI: 10.1186/s12915-021-01196-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of the brain and its major neuropils in Panarthropoda (comprising Arthropoda, Tardigrada and Onychophora) remains enigmatic. As one of the closest relatives of arthropods, onychophorans are regarded as indispensable for a broad understanding of the evolution of panarthropod organ systems, including the brain, whose anatomical and functional organisation is often used to gain insights into evolutionary relations. However, while numerous recent studies have clarified the organisation of many arthropod nervous systems, a detailed investigation of the onychophoran brain with current state-of-the-art approaches is lacking, and further inconsistencies in nomenclature and interpretation hamper its understanding. To clarify the origins and homology of cerebral structures across panarthropods, we analysed the brain architecture in the onychophoran Euperipatoides rowelli by combining X-ray micro-computed tomography, histology, immunohistochemistry, confocal microscopy, and three-dimensional reconstruction. RESULTS Here, we use this detailed information to generate a consistent glossary for neuroanatomical studies of Onychophora. In addition, we report novel cerebral structures, provide novel details on previously known brain areas, and characterise further structures and neuropils in order to improve the reproducibility of neuroanatomical observations. Our findings support homology of mushroom bodies and central bodies in onychophorans and arthropods. Their antennal nerve cords and olfactory lobes most likely evolved independently. In contrast to previous reports, we found no evidence for second-order visual neuropils, or a frontal ganglion in the velvet worm brain. CONCLUSION We imaged the velvet worm nervous system at an unprecedented level of detail and compiled a comprehensive glossary of known and previously uncharacterised neuroanatomical structures to provide an in-depth characterisation of the onychophoran brain architecture. We expect that our data will improve the reproducibility and comparability of future neuroanatomical studies.
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Affiliation(s)
- Christine Martin
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany.
| | - Henry Jahn
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany
| | - Mercedes Klein
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany
| | - Jörg U Hammel
- Institute of Materials Physics, Helmholtz-Zentrum hereon, 21502, Geesthacht, Germany
| | - Paul A Stevenson
- Physiology of Animals and Behaviour, Institute of Biology, University of Leipzig, 04103, Leipzig, Germany
| | - Uwe Homberg
- Department of Biology, Animal Physiology, Philipps-Universität Marburg, 35043, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus Liebig University Giessen, 35032, Marburg, Germany
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, 34132, Kassel, Germany.
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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Baker CM, Buckman-Young RS, Costa CS, Giribet G. Phylogenomic Analysis of Velvet Worms (Onychophora) Uncovers an Evolutionary Radiation in the Neotropics. Mol Biol Evol 2021; 38:5391-5404. [PMID: 34427671 PMCID: PMC8662635 DOI: 10.1093/molbev/msab251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Onychophora ("velvet worms") are charismatic soil invertebrates known for their status as a "living fossil," their phylogenetic affiliation to arthropods, and their distinctive biogeographic patterns. However, several aspects of their internal phylogenetic relationships remain unresolved, limiting our understanding of the group's evolutionary history, particularly with regard to changes in reproductive mode and dispersal ability. To address these gaps, we used RNA sequencing and phylogenomic analysis of transcriptomes to reconstruct the evolutionary relationships and infer divergence times within the phylum. We recovered a fully resolved and well-supported phylogeny for the circum-Antarctic family Peripatopsidae, which retains signals of Gondwanan vicariance and showcases the evolutionary lability of reproductive mode in the family. Within the Neotropical clade of Peripatidae, though, we found that amino acid-translated sequence data masked nearly all phylogenetic signal, resulting in highly unstable and poorly supported relationships. Analyses using nucleotide sequence data were able to resolve many more relationships, though we still saw discordant phylogenetic signal between genes, probably indicative of a rapid, mid-Cretaceous radiation in the group. Finally, we hypothesize that the unique reproductive mode of placentotrophic viviparity found in all Neotropical peripatids may have facilitated the multiple inferred instances of over-water dispersal and establishment on oceanic islands.
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Affiliation(s)
- Caitlin M Baker
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Rebecca S Buckman-Young
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Cristiano S Costa
- Laboratório de Sistemática e Taxonomia de Artrópodes Terrestres, Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
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Lafuente E, Lürig MD, Rövekamp M, Matthews B, Buser C, Vorburger C, Räsänen K. Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.
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Lei Y, Xu Y, Zhang J, Song J, Wu J. Herbivory-induced systemic signals are likely to be evolutionarily conserved in euphyllophytes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7274-7284. [PMID: 34293107 PMCID: PMC8547156 DOI: 10.1093/jxb/erab349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Herbivory-induced systemic signaling has been demonstrated in monocots and dicots, and is essential for plant defense against insects. However, the nature and evolution of herbivory-induced systemic signals remain unclear. Grafting is widely used for studying systemic signaling; however, grafting between dicot plants from different families is difficult, and grafting is impossible for monocots. In this study, we took advantage of dodder's extraordinary capability of parasitizing various plant species. Field dodder (Cuscuta campestris) was employed to connect pairs of species that are phylogenetically very distant, ranging from fern to monocot and dicot plants, and so determine whether interplant signaling occurs after simulated herbivory. It was found that simulated herbivory-induced systemic signals can be transferred by dodder between a monocot and a dicot plant and even between a fern and a dicot plant, and the plants that received the systemic signals all exhibited elevated defenses. Thus, we inferred that the herbivory-induced systemic signals are likely to be evolutionarily well conserved among vascular plants. Importantly, we also demonstrate that the jasmonate pathway is probably an ancient regulator of the biosynthesis and/or transport of systemic signals in vascular plants. These findings provide new insight into the nature and evolution of systemic signaling.
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Affiliation(s)
- Yunting Lei
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxing Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxiong Zhang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Juan Song
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jianqiang Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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Mapalo MA, Robin N, Boudinot BE, Ortega-Hernández J, Barden P. A tardigrade in Dominican amber. Proc Biol Sci 2021; 288:20211760. [PMID: 34610770 PMCID: PMC8493197 DOI: 10.1098/rspb.2021.1760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/15/2021] [Indexed: 01/17/2023] Open
Abstract
Tardigrades are a diverse group of charismatic microscopic invertebrates that are best known for their ability to survive extreme conditions. Despite their long evolutionary history and global distribution in both aquatic and terrestrial environments, the tardigrade fossil record is exceedingly sparse. Molecular clocks estimate that tardigrades diverged from other panarthropod lineages before the Cambrian, but only two definitive crown-group representatives have been described to date, both from Cretaceous fossil deposits in North America. Here, we report a third fossil tardigrade from Miocene age Dominican amber. Paradoryphoribius chronocaribbeus gen. et sp. nov. is the first unambiguous fossil representative of the diverse superfamily Isohypsibioidea, as well as the first tardigrade fossil described from the Cenozoic. We propose that the patchy tardigrade fossil record can be explained by the preferential preservation of these microinvertebrates as amber inclusions, coupled with the scarcity of fossiliferous amber deposits before the Cretaceous.
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Affiliation(s)
- Marc A. Mapalo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Ninon Robin
- Directorate Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Brendon E. Boudinot
- Institut für Spezielle Zoologie und Evolutionsforschung, Friedrich-Schiller-Universität Jena, Jena, Germany
- University of California, Davis, Department of Entomology, One Shields Avenue, Davis 94596, CA, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Phillip Barden
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, USA
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Tihelka E, Cai C, Giacomelli M, Lozano-Fernandez J, Rota-Stabelli O, Huang D, Engel MS, Donoghue PCJ, Pisani D. The evolution of insect biodiversity. Curr Biol 2021; 31:R1299-R1311. [PMID: 34637741 DOI: 10.1016/j.cub.2021.08.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Insects comprise over half of all described animal species. Together with the Protura (coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form the Hexapoda, a terrestrial arthropod lineage characterised by possessing six legs. Exponential growth of genome-scale data for the hexapods has substantially altered our understanding of the origin and evolution of insect biodiversity. Phylogenomics has provided a new framework for reconstructing insect evolutionary history, resolving their position among the arthropods and some long-standing internal controversies such as the placement of the termites, twisted-winged insects, lice and fleas. However, despite the greatly increased size of phylogenomic datasets, contentious relationships among key insect clades remain unresolved. Further advances in insect phylogeny cannot rely on increased depth and breadth of genome and taxon sequencing. Improved modelling of the substitution process is fundamental to countering tree-reconstruction artefacts, while gene content, modelling of duplications and deletions, and comparative morphology all provide complementary lines of evidence to test hypotheses emerging from the analysis of sequence data. Finally, the integration of molecular and morphological data is key to the incorporation of fossil species within insect phylogeny. The emerging integrated framework of insect evolution will help explain the origins of insect megadiversity in terms of the evolution of their body plan, species diversity and ecology. Future studies of insect phylogeny should build upon an experimental, hypothesis-driven approach where the robustness of hypotheses generated is tested against increasingly realistic evolutionary models as well as complementary sources of phylogenetic evidence.
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Affiliation(s)
- Erik Tihelka
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | - Chenyang Cai
- School of Earth Sciences, University of Bristol, Bristol, UK; State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.
| | | | - Jesus Lozano-Fernandez
- School of Biological Sciences, University of Bristol, Bristol, UK; Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige, Italy; Center Agriculture Food Environment, University of Trento, 38010 San Michele all Adige, Italy
| | - Diying Huang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, and Centre for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China
| | - Michael S Engel
- Division of Entomology, Natural History Museum, University of Kansas, Lawrence, KS, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, UK; School of Biological Sciences, University of Bristol, Bristol, UK.
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Lima LF, Torres AQ, Jardim R, Mesquita RD, Schama R. Evolution of Toll, Spatzle and MyD88 in insects: the problem of the Diptera bias. BMC Genomics 2021; 22:562. [PMID: 34289811 PMCID: PMC8296651 DOI: 10.1186/s12864-021-07886-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Arthropoda, the most numerous and diverse metazoan phylum, has species in many habitats where they encounter various microorganisms and, as a result, mechanisms for pathogen recognition and elimination have evolved. The Toll pathway, involved in the innate immune system, was first described as part of the developmental pathway for dorsal-ventral differentiation in Drosophila. Its later discovery in vertebrates suggested that this system was extremely conserved. However, there is variation in presence/absence, copy number and sequence divergence in various genes along the pathway. As most studies have only focused on Diptera, for a comprehensive and accurate homology-based approach it is important to understand gene function in a number of different species and, in a group as diverse as insects, the use of species belonging to different taxonomic groups is essential. RESULTS We evaluated the diversity of Toll pathway gene families in 39 Arthropod genomes, encompassing 13 different Insect Orders. Through computational methods, we shed some light into the evolution and functional annotation of protein families involved in the Toll pathway innate immune response. Our data indicates that: 1) intracellular proteins of the Toll pathway show mostly species-specific expansions; 2) the different Toll subfamilies seem to have distinct evolutionary backgrounds; 3) patterns of gene expansion observed in the Toll phylogenetic tree indicate that homology based methods of functional inference might not be accurate for some subfamilies; 4) Spatzle subfamilies are highly divergent and also pose a problem for homology based inference; 5) Spatzle subfamilies should not be analyzed together in the same phylogenetic framework; 6) network analyses seem to be a good first step in inferring functional groups in these cases. We specifically show that understanding Drosophila's Toll functions might not indicate the same function in other species. CONCLUSIONS Our results show the importance of using species representing the different orders to better understand insect gene content, origin and evolution. More specifically, in intracellular Toll pathway gene families the presence of orthologues has important implications for homology based functional inference. Also, the different evolutionary backgrounds of Toll gene subfamilies should be taken into consideration when functional studies are performed, especially for TOLL9, TOLL, TOLL2_7, and the new TOLL10 clade. The presence of Diptera specific clades or the ones lacking Diptera species show the importance of overcoming the Diptera bias when performing functional characterization of Toll pathways.
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Affiliation(s)
- Letícia Ferreira Lima
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - André Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil
| | - Rafael Dias Mesquita
- Laboratório de Bioinformática, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, Oswaldo Cruz Foundation, Fiocruz, Rio de Janeiro, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular-INCT-EM, Rio de Janeiro, Brazil.
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Morek W, Surmacz B, López‐López A, Michalczyk Ł. "Everything is not everywhere": Time-calibrated phylogeography of the genus Milnesium (Tardigrada). Mol Ecol 2021; 30:3590-3609. [PMID: 33966339 PMCID: PMC8361735 DOI: 10.1111/mec.15951] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/31/2021] [Accepted: 04/29/2021] [Indexed: 11/29/2022]
Abstract
There is ample evidence that macroscopic animals form geographic clusters termed as zoogeographic realms, whereas distributions of species of microscopic animals are still poorly understood. The common view has been that micrometazoans, thanks to their putatively excellent dispersal abilities, are subject to the "Everything is everywhere but environment selects" hypothesis (EiE). One of such groups, <1 mm in length, are limnoterrestrial water bears (Tardigrada), which can additionally enter cryptobiosis that should further enhance their potential for long distance dispersion (e.g., by wind). However, an increasing number of studies, including the most recent phylogeny of the eutardigrade genus Milnesium, seem to question the general applicability of the EiE hypothesis to tardigrade species. Nevertheless, all Milnesium phylogenies published to date were based on a limited number of populations, which are likely to falsely suggest limited geographic ranges. Thus, in order to test the EiE hypothesis more confidently, we considerably enlarged the Milnesium data set both taxonomically and geographically, and analysed it in tandem with climate type and reproductive mode. Additionally, we time-calibrated our phylogeny to align it with major geological events. Our results show that, although cases of long distance dispersal are present, they seem to be rare and mostly ancient. Overall, Milnesium species are restricted to single zoogeographic realms, which suggests that these tardigrades have limited dispersal abilities. Finally, our results also suggest that the breakdown of Gondwana may have influenced the evolutionary history of Milnesium. In conclusion, phylogenetic relationships within the genus seem to be determined mainly by paleogeography.
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Affiliation(s)
- Witold Morek
- Department of Invertebrate EvolutionInstitute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Bartłomiej Surmacz
- Department of Invertebrate EvolutionInstitute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Alejandro López‐López
- Department of Invertebrate EvolutionInstitute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
| | - Łukasz Michalczyk
- Department of Invertebrate EvolutionInstitute of Zoology and Biomedical ResearchFaculty of BiologyJagiellonian UniversityKrakówPoland
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41
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Koiwai K, Koyama T, Tsuda S, Toyoda A, Kikuchi K, Suzuki H, Kawano R. Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process. eLife 2021; 10:e66954. [PMID: 34132195 PMCID: PMC8266392 DOI: 10.7554/elife.66954] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing revealed six types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and predicted the differentiation pathways involved in their maturation. We also predicted cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.
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Affiliation(s)
- Keiichiro Koiwai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
- Laboratory of Genome Science, Tokyo University of Marine Science and TechnologyMinatoJapan
| | - Takashi Koyama
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
- Graduate School of Fisheries and Environmental Sciences, Nagasaki UniversityNagasakiJapan
| | | | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of GeneticsMishimaJapan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of TokyoHamamatsuJapan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo UniversityBunkyoJapan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and TechnologyKoganeiJapan
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Medina-Jiménez BI, Budd GE, Janssen R. Panarthropod tiptop/teashirt and spalt orthologs and their potential role as "trunk"-selector genes. EvoDevo 2021; 12:7. [PMID: 34078450 PMCID: PMC8173736 DOI: 10.1186/s13227-021-00177-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the vinegar fly Drosophila melanogaster, the homeodomain containing transcription factor Teashirt (Tsh) appears to specify trunk identity in concert with the function of the Hox genes. While in Drosophila there is a second gene closely related to tsh, called tiptop (tio), in other arthropods species only one copy exists (called tio/tsh). The expression of tsh and tio/tsh, respectively, is surprisingly similar among arthropods suggesting that its function as trunk selector gene may be conserved. Other research, for example on the beetle Tribolium castaneum, questions even conservation of Tsh function among insects. The zinc-finger transcription factor Spalt (Sal) is involved in the regulation of Drosophila tsh, but this regulatory interaction does not appear to be conserved in Tribolium either. Whether the function and interaction of tsh and sal as potential trunk-specifiers, however, is conserved is still unclear because comparative studies on sal expression (except for Tribolium) are lacking, and functional data are (if at all existing) restricted to Insecta. RESULTS Here, we provide additional data on arthropod tsh expression, show the first data on onychophoran tio/tsh expression, and provide a comprehensive investigation on sal expression patterns in arthropods and an onychophoran. CONCLUSIONS Our data support the idea that tio/tsh genes are involved in the development of "trunk" segments by regulating limb development. Our data suggest further that the function of Sal is indeed unlikely to be conserved in trunk vs head development like in Drosophila, but early expression of sal is in line with a potential homeotic function, at least in Arthropoda.
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Affiliation(s)
- Brenda I Medina-Jiménez
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, Sweden
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, Sweden
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, Sweden.
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Beavan AJS, Pisani D, Donoghue PCJ. Diversification dynamics of total-, stem-, and crown-groups are compatible with molecular clock estimates of divergence times. SCIENCE ADVANCES 2021; 7:eabf2257. [PMID: 34117058 PMCID: PMC8195484 DOI: 10.1126/sciadv.abf2257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/28/2021] [Indexed: 05/05/2023]
Abstract
Molecular evolutionary time scales are expected to predate the fossil evidence, but, particularly for major evolutionary radiations, they can imply extremely protracted stem lineages predating the origin of living clades, leading to claims of systematic overestimation of divergence times. We use macroevolutionary birth-death models to describe the range of total-group and crown-group ages expected under constant rates of speciation and extinction. We extend current predictions on origination times for crown- and total-groups, and extinction of stem-groups, demonstrating that there is broad variance in these predictions. Under constant rates of speciation and extinction, we show that the distribution of expected arthropod total-group ages is consistent with molecular clock estimates. The fossil record cannot be read literally, and our results preclude attempts to interpret the antiquity of clades based on the co-occurrence of stem- and crown-representatives.
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Affiliation(s)
- Alan J S Beavan
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Davide Pisani
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
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Xie Y, Zhang P, Zhang L. Genome-Wide Transcriptional Responses of Marine Nematode Litoditis marina to Hyposaline and Hypersaline Stresses. Front Physiol 2021; 12:672099. [PMID: 34017268 PMCID: PMC8129518 DOI: 10.3389/fphys.2021.672099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Maintenance of osmotic homeostasis is essential for all organisms, especially for marine animals in the ocean with 3% salinity or higher. However, the underlying molecular mechanisms that how marine animals adapt to high salinity environment compared to their terrestrial relatives, remain elusive. Here, we investigated marine animal’s genome-wide transcriptional responses to salinity stresses using an emerging marine nematode model Litoditis marina. We found that the transthyretin-like family genes were significantly increased in both hyposaline and hypersaline conditions, while multiple neurotransmitter receptor and ion transporter genes were down-regulated in both conditions, suggesting the existence of conserved strategies for response to stressful salinity environments in L. marina. Unsaturated fatty acids biosynthesis related genes, neuronal related tubulins and intraflagellar transport genes were specifically up-regulated in hyposaline treated worms. By contrast, cuticle related collagen genes were enriched and up-regulated for hypersaline response. Given a wide range of salinity tolerance of the marine nematodes, this study and further genetic analysis of key gene(s) of osmoregulation in L. marina will likely provide important insights into biological evolution and environmental adaptation mechanisms in nematodes and other invertebrate animals in general.
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Affiliation(s)
- Yusu Xie
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Pengchi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liusuo Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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45
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Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1236-1280. [PMID: 33893979 DOI: 10.1007/s11427-020-1915-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/16/2021] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.
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46
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Shen C, Tang D, Zhang Y, Wu L, Luo Y, Tang B, Wang Z. Identification of putative ingestion-related olfactory receptor genes in the Chinese mitten crab (Eriocheir japonica sinensis). Genes Genomics 2021; 43:479-490. [PMID: 33689153 DOI: 10.1007/s13258-021-01065-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Olfaction plays a central role in mating, spawning, obtaining food and escaping predators, which is essential for survival and reproduction of animals. The nature of the olfactory perception in crabs, which is a major group of crustaceans, has remained elusive. OBJECTIVE This project aims to explore the molecular mechanism of olfaction in crabs and further improve our understanding of olfactory perception in crustaceans. METHODS The olfactory receptors and ingestion-related gene expression in Eriocheir japonica sinensis were studied by transcriptomic techniques. The de novo assembly, annotation and functional evaluation were performed with bioinformatics tools. RESULTS A series of chemosensory receptors associated with olfaction were identified including 33 EsIRs, 24 EsIGluRs, 58 EsVIGluRs, 1 EsOR and 1 EsGC-D. We found IRs were key odorant receptors demonstrating a specific species evolutionary trend in crustaceans. Furthermore, we identified ORs in E. j. sinensis and Litopenaeus vannamei. The incomplete EsOR and LvOR1 structures implied that ORs exist in crustaceans, and may have been degenerated or even lost in the olfactory evolutionary process. In addition, comparative transcriptome analysises demonstrated two possible olfactory transduction pathways of E. j. sinensis: the cGMP-mediated olfactory pathway related to vegetable odor molecules and the cAMP-mediated olfactory pathway related to meat odor molecules. The above results were consistent with its omnivorous ingestion of E. j. sinensis. CONCLUSIONS Our study revealed the unique olfactory molecular mechanism of omnivorous crabs and provided valuable information for further functional research on the chemoreception mechanisms in crustaceans.
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Affiliation(s)
- Chenchen Shen
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Dan Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, Jiangsu, China
| | - Yiping Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Lv Wu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Yaqi Luo
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China
| | - Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng, 224001, Jiangsu, China.
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47
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Zadra N, Rizzoli A, Rota-Stabelli O. Chronological Incongruences between Mitochondrial and Nuclear Phylogenies of Aedes Mosquitoes. Life (Basel) 2021; 11:life11030181. [PMID: 33669100 PMCID: PMC7996624 DOI: 10.3390/life11030181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/12/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoes.
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Affiliation(s)
- Nicola Zadra
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Povo (TN), Italy
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all Adige (TN), Italy; (N.Z.); (A.R.)
- Department of Cellular, Computational and Integrative Biology—CIBIO, University of Trento, 38123 Povo (TN), Italy
- Center Agriculture Food Environment—C3A, University of Trento, 38010 San Michele all Adige (TN), Italy
- Correspondence:
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48
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Hilken G, Rosenberg J, Edgecombe GD, Blüml V, Hammel JU, Hasenberg A, Sombke A. The tracheal system of scutigeromorph centipedes and the evolution of respiratory systems of myriapods. ARTHROPOD STRUCTURE & DEVELOPMENT 2021; 60:101006. [PMID: 33246291 DOI: 10.1016/j.asd.2020.101006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/30/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
The tracheal system of scutigeromorph centipedes (Chilopoda) is special, as it consists of dorsally arranged unpaired spiracles. In this study, we investigate the tracheal systems of five different scutigeromorph species. They are strikingly similar to each other but depict unique characters compared to the tracheal systems of pleurostigmophoran centipedes, which has engendered an ongoing debate over a single versus independent origin of tracheal systems in Chilopoda. Up to now, only the respiratory system of Scutigera coleoptrata was investigated intensively using LM-, TEM-, and SEM-techniques. We supplement this with data for species from all three families of Scutigeromorpha. These reveal interspecific differences in atrial width and the shape and branching pattern of the tracheal tubules. Further, we investigated the tracheal system of Scutigera coleoptrata with three additional techniques: light sheet microscopy, microCT and synchrotron radiation based microCT analysis. This set of techniques allows a comparison between fresh versus fixed and dried material. The question of a unique vs. multiple origin of tracheal systems in centipedes and in Myriapoda as a whole is discussed with regard to their structural similarities and differences and the presence of hemocyanin as an oxygen carrier. We used morphological and molecular data and the fossil record to evaluate the alternative hypotheses.
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Affiliation(s)
- Gero Hilken
- Central Animal Laboratory, University Clinic, University Duisburg-Essen, Hufelandstraße 55, 45122, Essen, Germany.
| | | | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, London, SW7 5BD, United Kingdom
| | - Valentin Blüml
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria
| | - Jörg U Hammel
- X-ray Imaging with Synchrotron Radiation, Helmholz-Zentrum Geesthacht, Institute of Materials Research, Max-Planck-Straße 1, 21502, Geesthacht, Germany
| | - Anja Hasenberg
- Institute for Experimental Immunology and Imaging, University Clinic, University Duisburg-Essen, Universitätsstraße 2, 45141, Essen, Germany
| | - Andy Sombke
- Department of Evolutionary Biology, Integrative Zoology, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
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Howard RJ, Edgecombe GD, Shi X, Hou X, Ma X. Ancestral morphology of Ecdysozoa constrained by an early Cambrian stem group ecdysozoan. BMC Evol Biol 2020; 20:156. [PMID: 33228518 PMCID: PMC7684930 DOI: 10.1186/s12862-020-01720-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 11/08/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ecdysozoa are the moulting protostomes, including arthropods, tardigrades, and nematodes. Both the molecular and fossil records indicate that Ecdysozoa is an ancient group originating in the terminal Proterozoic, and exceptional fossil biotas show their dominance and diversity at the beginning of the Phanerozoic. However, the nature of the ecdysozoan common ancestor has been difficult to ascertain due to the extreme morphological diversity of extant Ecdysozoa, and the lack of early diverging taxa in ancient fossil biotas. RESULTS Here we re-describe Acosmia maotiania from the early Cambrian Chengjiang Biota of Yunnan Province, China and assign it to stem group Ecdysozoa. Acosmia features a two-part body, with an anterior proboscis bearing a terminal mouth and muscular pharynx, and a posterior annulated trunk with a through gut. Morphological phylogenetic analyses of the protostomes using parsimony, maximum likelihood and Bayesian inference, with coding informed by published experimental decay studies, each placed Acosmia as sister taxon to Cycloneuralia + Panarthropoda-i.e. stem group Ecdysozoa. Ancestral state probabilities were calculated for key ecdysozoan nodes, in order to test characters inferred from fossils to be ancestral for Ecdysozoa. Results support an ancestor of crown group ecdysozoans sharing an annulated vermiform body with a terminal mouth like Acosmia, but also possessing the pharyngeal armature and circumoral structures characteristic of Cambrian cycloneuralians and lobopodians. CONCLUSIONS Acosmia is the first taxon placed in the ecdysozoan stem group and provides a constraint to test hypotheses on the early evolution of Ecdysozoa. Our study suggests acquisition of pharyngeal armature, and therefore a change in feeding strategy (e.g. predation), may have characterised the origin and radiation of crown group ecdysozoans from Acosmia-like ancestors.
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Affiliation(s)
- Richard J Howard
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Chenggong Campus, Kunming, 650500, China
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, TR10 9TA, UK
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Gregory D Edgecombe
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Chenggong Campus, Kunming, 650500, China
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Xiaomei Shi
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Chenggong Campus, Kunming, 650500, China
- Yunnan Key Laboratory for Palaeobiology, Institute of Palaeontology, Yunnan University, Chenggong Campus, Kunming, 650500, China
| | - Xianguang Hou
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Chenggong Campus, Kunming, 650500, China.
- Yunnan Key Laboratory for Palaeobiology, Institute of Palaeontology, Yunnan University, Chenggong Campus, Kunming, 650500, China.
| | - Xiaoya Ma
- MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Chenggong Campus, Kunming, 650500, China.
- Yunnan Key Laboratory for Palaeobiology, Institute of Palaeontology, Yunnan University, Chenggong Campus, Kunming, 650500, China.
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall, TR10 9TA, UK.
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50
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Arribas P, Andújar C, Moraza ML, Linard B, Emerson BC, Vogler AP. Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari. Mol Biol Evol 2020; 37:683-694. [PMID: 31670799 DOI: 10.1093/molbev/msz255] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - María Lourdes Moraza
- Departamento de Biología Ambiental, Universidad de Navarra, Facultad de Ciencias, Pamplona, Spain
| | - Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,LIRMM, Université de Montpellier, CNRS, Montpellier, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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