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Yue T, Si W, Keller A, Yang C, Bloomfield-Gadêlha H, Rossiter J. Bioinspired multiscale adaptive suction on complex dry surfaces enhanced by regulated water secretion. Proc Natl Acad Sci U S A 2024; 121:e2314359121. [PMID: 38557166 PMCID: PMC11032437 DOI: 10.1073/pnas.2314359121] [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: 08/20/2023] [Accepted: 01/16/2024] [Indexed: 04/04/2024] Open
Abstract
Suction is a highly evolved biological adhesion strategy for soft-body organisms to achieve strong grasping on various objects. Biological suckers can adaptively attach to dry complex surfaces such as rocks and shells, which are extremely challenging for current artificial suction cups. Although the adaptive suction of biological suckers is believed to be the result of their soft body's mechanical deformation, some studies imply that in-sucker mucus secretion may be another critical factor in helping attach to complex surfaces, thanks to its high viscosity. Inspired by the combined action of biological suckers' soft bodies and mucus secretion, we propose a multiscale suction mechanism which successfully achieves strong adaptive suction on dry complex surfaces which are both highly curved and rough, such as a stone. The proposed multiscale suction mechanism is an organic combination of mechanical conformation and regulated water seal. Multilayer soft materials first generate a rough mechanical conformation to the substrate, reducing leaking apertures to micrometres (~10 µm). The remaining micron-sized apertures are then sealed by regulated water secretion from an artificial fluidic system based on the physical model, thereby the suction cup achieves long suction longevity on complex surfaces but minimal overflow. We discuss its physical principles and demonstrate its practical application as a robotic gripper on a wide range of complex dry surfaces. We believe the presented multiscale adaptive suction mechanism is a powerful unique adaptive suction strategy which may be instrumental in the development of versatile soft adhesion.
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Affiliation(s)
- Tianqi Yue
- School of Engineering Mathematics and Technology, and Bristol Robotics Laboratory, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Weiyong Si
- Faculty of Environment and Technology, and Bristol Robotics Laboratory, University of the West of England, BristolBS16 1QY, United Kingdom
- School of Computer Science and Electronic Engineering, University of Essex, EssexCO4 3SQ, United Kingdom
| | - Alex Keller
- School of Engineering Mathematics and Technology, and Bristol Robotics Laboratory, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Chenguang Yang
- Faculty of Environment and Technology, and Bristol Robotics Laboratory, University of the West of England, BristolBS16 1QY, United Kingdom
| | - Hermes Bloomfield-Gadêlha
- School of Engineering Mathematics and Technology, and Bristol Robotics Laboratory, University of Bristol, Bristol BS8 1TW, United Kingdom
| | - Jonathan Rossiter
- School of Engineering Mathematics and Technology, and Bristol Robotics Laboratory, University of Bristol, Bristol BS8 1TW, United Kingdom
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2
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Holzem M, Boutros M, Holstein TW. The origin and evolution of Wnt signalling. Nat Rev Genet 2024:10.1038/s41576-024-00699-w. [PMID: 38374446 DOI: 10.1038/s41576-024-00699-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
The Wnt signal transduction pathway has essential roles in the formation of the primary body axis during development, cellular differentiation and tissue homeostasis. This animal-specific pathway has been studied extensively in contexts ranging from developmental biology to medicine for more than 40 years. Despite its physiological importance, an understanding of the evolutionary origin and primary function of Wnt signalling has begun to emerge only recently. Recent studies on very basal metazoan species have shown high levels of conservation of components of both canonical and non-canonical Wnt signalling pathways. Furthermore, some pathway proteins have been described also in non-animal species, suggesting that recruitment and functional adaptation of these factors has occurred in metazoans. In this Review, we summarize the current state of research regarding the evolutionary origin of Wnt signalling, its ancestral function and the characteristics of the primal Wnt ligand, with emphasis on the importance of genomic studies in various pre-metazoan and basal metazoan species.
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Affiliation(s)
- Michaela Holzem
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
- Department of Cell and Molecular Biology & BioQuant, Heidelberg University, Heidelberg, Germany.
- Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany.
- Institute for Human Genetics, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany.
| | - Michael Boutros
- Division of Signalling and Functional Genomics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology & BioQuant, Heidelberg University, Heidelberg, Germany
- Faculty of Medicine Mannheim, Heidelberg University, Heidelberg, Germany
- Institute for Human Genetics, Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas W Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
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3
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BMC Biol 2024; 22:9. [PMID: 38233809 PMCID: PMC10795318 DOI: 10.1186/s12915-024-01814-3] [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: 08/07/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA.
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
| | - Robin A Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Paul S Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
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Amplatz K, Zieger E, Abed-Navandi D, Weissenbacher A, Wanninger A. Neuromuscular development in the emerging scyphozoan model system, Cassiopea xamachana: implications for the evolution of cnidarian nervous systems. Front Neurosci 2024; 17:1324980. [PMID: 38274504 PMCID: PMC10808518 DOI: 10.3389/fnins.2023.1324980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
The scyphozoan Cassiopea xamachana is an emerging cnidarian model system for studying regeneration, animal-algae symbiotic relationships, and various aspects of evolutionary biology including the early emergence of animal nervous systems. Cassiopea has a life cycle similar to other scyphozoans, which includes the alternation between a sessile, asexual form (polyp) and a sexually reproducing stage, the medusa. The transition between the two forms is called strobilation, where the polyp releases a miniature medusa, the iconic ephyra, that subsequently develops into the adult medusa. In addition, Cassiopea polyps may reproduce asexually by budding off free-swimming so-called planuloid buds. While the development of planuloid buds and polyps has been studied in some detail, little is known about the ontogeny of the sexually produced planula larva. Using immunofluorescence labeling and confocal microscopy, we examined neuromuscular development during metamorphosis of the planula larva into the juvenile polyp in C. xamachana. For this purpose, we used tyrosinated α-tubulin-, FMRFamide- and serotonin-like immunoreactivity together with phalloidin labeling. Our results show a planula nervous system that consists of a basiectodermal neural plexus with mostly longitudinally oriented neurites. This neural meshwork is connected to sensory neurons in the superficial stratum of the ectoderm, which are exclusively localized in the aboral half of the larva. During settlement, this aborally concentrated nervous system of the planula is replaced completely by the orally concentrated nervous system of the polyp. Adult polyps show an extensive nerve net with a loose concentration around the oral disc. These findings are consistent with data from other scyphozoans and most likely constitute a conserved feature of scyphozoan discomedusae. Taken together, the data currently available suggest an aborally concentrated nervous system including sensory cells as part of the neural ground pattern of cnidarian planula larvae. The reorganization of the nervous system from anterior to posterior in planula-to-polyp metamorphosis most likely also constitutes an ancestral trait in cnidarian evolution.
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Affiliation(s)
- Klara Amplatz
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Elisabeth Zieger
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Daniel Abed-Navandi
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
- Haus des Meeres, Vienna, Austria
| | | | - Andreas Wanninger
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
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5
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Mamut R, Anwar G, Wang L, Fang J. The mitogenomes characterization of two Peltigera species (Peltigera elisabethae and Peltigera polydactylon) and comparative mitogenomic analyses of six Peltigera. J Appl Genet 2023; 64:819-829. [PMID: 37821790 DOI: 10.1007/s13353-023-00791-7] [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: 05/08/2023] [Revised: 09/15/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
In the present study, the mitochondrial genomes of Peltigera elisabethae and P. polydactylon were sequenced and assembled. The two mitogenomes were composed of circular DNA molecules, with sizes of 64,034 bp and 59,208 bp, respectively. Comparative analysis showed that the genome size, GC content, GC skew, and AT skew varied between the two mitochondrial genomes. In codon analysis, phenylalanine (Phe), isoleucine (Ile), and leucine (Leu) were most frequently used in six Peltigera genomes. Evolutionary analysis showed that all 14 protein-coding genes (PCGs) were subject to purifying selection in the six Peltigera species. Regarding gene rearrangement, the PCGs of Peltigera had the same gene sequence and gene content, and a few intron sequences and spacer sequences were rearranged in Peltigera. In the phylogenetic analysis, we used Bayesian and ML methods to construct a phylogenetic tree. Two phylogenetic trees with consistent topology with high support indicate that mitochondrial genes were reliable molecular markers for analyzing the phylogenetic relationships. The present study enriches the mitochondrial genome data of Peltigera and promotes further understanding of the genetics and evolution of the Peltigera genus.
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Affiliation(s)
- Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China.
| | - Gulmira Anwar
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
| | - Lidan Wang
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
| | - Jinjin Fang
- College of Life Sciences and Technology, Xinjiang University, No.777 Huarui Street, Urumchi, 830017, Xinjiang, China
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6
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Goodheart JA, Rio RA, Taraporevala NF, Fiorenza RA, Barnes SR, Morrill K, Jacob MAC, Whitesel C, Masterson P, Batzel GO, Johnston HT, Ramirez MD, Katz PS, Lyons DC. A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552006. [PMID: 38014205 PMCID: PMC10680569 DOI: 10.1101/2023.08.04.552006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.
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Affiliation(s)
- Jessica A. Goodheart
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Robin A. Rio
- Bioengineering Department, Stanford University, Stanford, CA, USA
| | - Neville F. Taraporevala
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Wildland Resources, Utah State University, Logan, UT, USA
| | - Rose A. Fiorenza
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Seth R. Barnes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kevin Morrill
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Mark Allan C. Jacob
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl Whitesel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Park Masterson
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Grant O. Batzel
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hereroa T. Johnston
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - M. Desmond Ramirez
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Paul S. Katz
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Deirdre C. Lyons
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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7
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Smith FW, Game M, Mapalo MA, Chavarria RA, Harrison TR, Janssen R. Developmental and genomic insight into the origin of the tardigrade body plan. Evol Dev 2023. [PMID: 37721221 DOI: 10.1111/ede.12457] [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: 05/05/2023] [Revised: 08/11/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Tardigrada is an ancient lineage of miniaturized animals. As an outgroup of the well-studied Arthropoda and Onychophora, studies of tardigrades hold the potential to reveal important insights into body plan evolution in Panarthropoda. Previous studies have revealed interesting facets of tardigrade development and genomics that suggest that a highly compact body plan is a derived condition of this lineage, rather than it representing an ancestral state of Panarthropoda. This conclusion was based on studies of several species from Eutardigrada. We review these studies and expand on them by analyzing the publicly available genome and transcriptome assemblies of Echiniscus testudo, a representative of Heterotardigrada. These new analyses allow us to phylogenetically reconstruct important features of genome evolution in Tardigrada. We use available data from tardigrades to interrogate several recent models of body plan evolution in Panarthropoda. Although anterior segments of panarthropods are highly diverse in terms of anatomy and development, both within individuals and between species, we conclude that a simple one-to-one alignment of anterior segments across Panarthropoda is the best available model of segmental homology. In addition to providing important insight into body plan diversification within Panarthropoda, we speculate that studies of tardigrades may reveal generalizable pathways to miniaturization.
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Affiliation(s)
- Frank W Smith
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Mandy Game
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Marc A Mapalo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Raul A Chavarria
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Taylor R Harrison
- Biology Department, University of North Florida, Jacksonville, Florida, USA
| | - Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden
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8
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Hulett RE, Gehrke AR, Gompers A, Rivera-López C, Srivastava M. A wound-induced differentiation trajectory for neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540286. [PMID: 37214981 PMCID: PMC10197691 DOI: 10.1101/2023.05.10.540286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully-functional new organs, de novo . The regeneration of a new brain requires the formation of diverse neuronal cell types and their assembly into an organized structure and correctly-wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neuronal subpopulations, however how these transcriptional programs are initiated upon amputation remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia , to study wound-induced transcriptional regulatory events that lead to the production of neurons. Footprinting analysis using chromatin accessibility data on an improved genome assembly revealed that binding sites for the NFY transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal functional. Single-cell transcriptome analysis combined with functional studies identified sox4 + stem cells as the likely progenitor population for multiple neuronal subtypes. Further, we found that wound-induced sox4 expression is likely under direct transcriptional control by NFY, uncovering a mechanism for how early wound-induced binding of a transcriptional regulator results in the initiation of a neuronal differentiation pathway. Highlights A new chromosome-scale assembly for Hofstenia enables comprehensive analysis of transcription factor binding during regeneration NFY motifs become dynamically bound by 1hpa in regenerating tail fragments, particularly in the loci of neural genes A sox4 + neural-specialized stem cell is identified using scRNA-seq sox4 is wound-induced and required for differentiation of multiple neural cell types NFY regulates wound-induced expression of sox4 during regeneration.
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Hulett RE, Kimura JO, Bolaños DM, Luo YJ, Rivera-López C, Ricci L, Srivastava M. Acoel single-cell atlas reveals expression dynamics and heterogeneity of adult pluripotent stem cells. Nat Commun 2023; 14:2612. [PMID: 37147314 PMCID: PMC10163032 DOI: 10.1038/s41467-023-38016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
Adult pluripotent stem cell (aPSC) populations underlie whole-body regeneration in many distantly-related animal lineages, but how the underlying cellular and molecular mechanisms compare across species is unknown. Here, we apply single-cell RNA sequencing to profile transcriptional cell states of the acoel worm Hofstenia miamia during postembryonic development and regeneration. We identify cell types shared across stages and their associated gene expression dynamics during regeneration. Functional studies confirm that the aPSCs, also known as neoblasts, are the source of differentiated cells and reveal transcription factors needed for differentiation. Subclustering of neoblasts recovers transcriptionally distinct subpopulations, the majority of which are likely specialized to differentiated lineages. One neoblast subset, showing enriched expression of the histone variant H3.3, appears to lack specialization. Altogether, the cell states identified in this study facilitate comparisons to other species and enable future studies of stem cell fate potentials.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
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10
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Temereva EN, Isaeva MA, Kosevich IA. Unusual lophophore innervation in ctenostome Flustrellidra hispida (Bryozoa). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:245-258. [PMID: 35662417 DOI: 10.1002/jez.b.23164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/13/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Since ctenostomes are traditionally regarded as an ancestral clade to some other bryozoan groups, the study of additional species may help to clarify questions on bryozoan evolution and phylogeny. One of these questions is the bryozoan lophophore evolution: whether it occurred through simplification or complication. The morphology and innervation of the ctenostome Flustrellidra hispida (Fabricius, 1780) lophophore have been studied with electron microscopy and immunocytochemistry with confocal laser scanning microscopy. Lophophore nervous system of F. hispida consists of several main nerve elements: cerebral ganglion, circumoral nerve ring, and the outer nerve ring. Serotonin-like immunoreactive perikarya, which connect with the circumoral nerve ring, bear the cilium that directs to the abfrontal side of the lophophore and extends between tentacle bases. The circumoral nerve ring gives rise to the intertentacular and frontal tentacle nerves. The outer nerve ring gives rise to the abfrontal neurites, which connect to the outer groups of perikarya and contribute to the formation of the abfrontal tentacle nerve. The outer nerve ring has been described before in other bryozoans, but it never contributes to the innervation of tentacles. The presence of the outer nerve ring participating in the innervation of tentacles makes the F. hispida lophophore nervous system particularly similar to the lophophore nervous system of phoronids. This similarity allows to suggest that organization of the F. hispida lophophore nervous system may reflect the ancestral state for all bryozoans. The possible scenario of evolutionary transformation of the lophophore nervous system within bryozoans is suggested.
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Affiliation(s)
- Elena N Temereva
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A Isaeva
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Igor A Kosevich
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
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11
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Burkhardt P, Colgren J, Medhus A, Digel L, Naumann B, Soto-Angel JJ, Nordmann EL, Sachkova MY, Kittelmann M. Syncytial nerve net in a ctenophore adds insights on the evolution of nervous systems. Science 2023; 380:293-297. [PMID: 37079688 DOI: 10.1126/science.ade5645] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
A fundamental breakthrough in neurobiology has been the formulation of the neuron doctrine by Santiago Ramón y Cajal, which stated that the nervous system is composed of discrete cells. Electron microscopy later confirmed the doctrine and allowed the identification of synaptic connections. In this work, we used volume electron microscopy and three-dimensional reconstructions to characterize the nerve net of a ctenophore, a marine invertebrate that belongs to one of the earliest-branching animal lineages. We found that neurons in the subepithelial nerve net have a continuous plasma membrane that forms a syncytium. Our findings suggest fundamental differences of nerve net architectures between ctenophores and cnidarians or bilaterians and offer an alternative perspective on neural network organization and neurotransmission.
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Affiliation(s)
- Pawel Burkhardt
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Jeffrey Colgren
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Astrid Medhus
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Leonid Digel
- Michael Sars Centre, University of Bergen, 5008 Bergen, Norway
| | - Benjamin Naumann
- Institut für Biowissenschaften, Allgemeine und Spezielle Zoologie, Universität Rostock, 18055 Rostock, Germany
| | | | | | | | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
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12
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Nakano H, Nakano A, Maeno A, Thorndyke MC. Induced spawning with gamete release from body ruptures during reproduction of Xenoturbella bocki. Commun Biol 2023; 6:172. [PMID: 36805023 PMCID: PMC9938242 DOI: 10.1038/s42003-023-04549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Xenoturbella is a marine invertebrate with a simple body plan, with recent phylogenomic studies suggesting that it forms the phylum Xenacoelomorpha together with the acoelomorphs. The phylogenetic position of the phylum is still under debate, whether it is an early branching bilaterian or a sister group to the Ambulacraria. Phylogenetic traits often appear during development, and larva resembling the cnidarian planula has been reported for Xenoturbella. However, subsequent developmental studies on Xenoturbella have been scarce. This is mainly due to the difficulties in collecting and keeping adult animals, resulting in the lack of data on the reproduction of the animal, such as the breeding season and the spawning pattern. Here we report on the reproduction of X. bocki and confirm that its breeding season is winter. Spawning induction resulted in gametes being released from body ruptures and not the mouth. No evidence supported the animal as a simultaneous hermaphrodite.
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Affiliation(s)
- Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan. .,Kristineberg Marine Research Station, University of Gothenburg, Kristineberg 566, Fiskebäckskil, 45178, Sweden.
| | - Ako Nakano
- grid.20515.330000 0001 2369 4728Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka 415-0025 Japan
| | - Akiteru Maeno
- grid.288127.60000 0004 0466 9350Cell Architecture Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540 Japan
| | - Michael C. Thorndyke
- grid.8761.80000 0000 9919 9582Kristineberg Marine Research Station, University of Gothenburg, Kristineberg 566, Fiskebäckskil, 45178 Sweden
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13
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Martinez P, Ustyantsev K, Biryukov M, Mouton S, Glasenburg L, Sprecher SG, Bailly X, Berezikov E. Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis. G3 (BETHESDA, MD.) 2023; 13:jkac336. [PMID: 36542495 PMCID: PMC9911081 DOI: 10.1093/g3journal/jkac336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in the range of 910-940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona 08193, Spain
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Mikhail Biryukov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Liza Glasenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Chemin du Musee 10, 1700 Fribourg, Switzerland
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) team, FR2424, CNRS/Sorbonne Université—Place Georges Teissier, 29680 Roscoff, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
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14
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Nanglu K, Cole SR, Wright DF, Souto C. Worms and gills, plates and spines: the evolutionary origins and incredible disparity of deuterostomes revealed by fossils, genes, and development. Biol Rev Camb Philos Soc 2023; 98:316-351. [PMID: 36257784 DOI: 10.1111/brv.12908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Deuterostomes are the major division of animal life which includes sea stars, acorn worms, and humans, among a wide variety of ecologically and morphologically disparate taxa. However, their early evolution is poorly understood, due in part to their disparity, which makes identifying commonalities difficult, as well as their relatively poor early fossil record. Here, we review the available morphological, palaeontological, developmental, and molecular data to establish a framework for exploring the origins of this important and enigmatic group. Recent fossil discoveries strongly support a vermiform ancestor to the group Hemichordata, and a fusiform active swimmer as ancestor to Chordata. The diverse and anatomically bewildering variety of forms among the early echinoderms show evidence of both bilateral and radial symmetry. We consider four characteristics most critical for understanding the form and function of the last common ancestor to Deuterostomia: Hox gene expression patterns, larval morphology, the capacity for biomineralization, and the morphology of the pharyngeal region. We posit a deuterostome last common ancestor with a similar antero-posterior gene regulatory system to that found in modern acorn worms and cephalochordates, a simple planktonic larval form, which was later elaborated in the ambulacrarian lineage, the ability to secrete calcium minerals in a limited fashion, and a pharyngeal respiratory region composed of simple pores. This animal was likely to be motile in adult form, as opposed to the sessile origins that have been historically suggested. Recent debates regarding deuterostome monophyly as well as the wide array of deuterostome-affiliated problematica further suggest the possibility that those features were not only present in the last common ancestor of Deuterostomia, but potentially in the ur-bilaterian. The morphology and development of the early deuterostomes, therefore, underpin some of the most significant questions in the study of metazoan evolution.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Selina R Cole
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - David F Wright
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, OK, 73072, USA.,School of Geosciences, University of Oklahoma, 100 E Boyd Street, Norman, OK, 73019, USA
| | - Camilla Souto
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, 10th & Constitution Avenue NW, Washington, DC, 20560, USA.,School of Natural Sciences & Mathematics, Stockton University, 101 Vera King Farris Dr, Galloway, NJ, 08205, USA
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15
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Juravel K, Porras L, Höhna S, Pisani D, Wörheide G. Exploring genome gene content and morphological analysis to test recalcitrant nodes in the animal phylogeny. PLoS One 2023; 18:e0282444. [PMID: 36952565 PMCID: PMC10035847 DOI: 10.1371/journal.pone.0282444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although datasets of several hundred thousand amino acids are nowadays routinely used to test phylogenetic hypotheses, key deep nodes in the metazoan tree remain unresolved: the root of animals, the root of Bilateria, and the monophyly of Deuterostomia. Instead of using the standard approach of amino acid datasets, we performed analyses of newly assembled genome gene content and morphological datasets to investigate these recalcitrant nodes in the phylogeny of animals. We explored extensively the choices for assembling the genome gene content dataset and model choices of morphological analyses. Our results are robust to these choices and provide additional insights into the early evolution of animals, they are consistent with sponges as the sister group of all the other animals, the worm-like bilaterian lineage Xenacoelomorpha as the sister group of the other Bilateria, and tentatively support monophyletic Deuterostomia.
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Affiliation(s)
- Ksenia Juravel
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Luis Porras
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Höhna
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
- SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, München, Germany
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16
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Abstract
Panarthropoda, the clade comprising the phyla Onychophora, Tardigrada and Euarthropoda, encompasses the largest majority of animal biodiversity. The relationships among the phyla are contested and resolution is key to understanding the evolutionary assembly of panarthropod bodyplans. Molecular phylogenetic analyses generally support monophyly of Onychophora and Euarthropoda to the exclusion of Tardigrada (Lobopodia hypothesis), which is also supported by some analyses of morphological data. However, analyses of morphological data have also been interpreted to support monophyly of Tardigrada and Euarthropoda to the exclusion of Onychophora (Tactopoda hypothesis). Support has also been found for a clade of Onychophora and Tardigrada that excludes Euarthropoda (Protarthropoda hypothesis). Here we show, using a diversity of phylogenetic inference methods, that morphological datasets cannot discriminate statistically between the Lobopodia, Tactopoda and Protarthropoda hypotheses. Since the relationships among the living clades of panarthropod phyla cannot be discriminated based on morphological data, we call into question the accuracy of morphology-based phylogenies of Panarthropoda that include fossil species and the evolutionary hypotheses based upon them.
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Affiliation(s)
- Ruolin Wu
- Bristol Palaeobiology Group, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK,School of Earth Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK,School of Biological Sciences, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C. J. Donoghue
- Bristol Palaeobiology Group, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK,School of Earth Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK
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17
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Brachiopod and mollusc biomineralisation is a conserved process that was lost in the phoronid-bryozoan stem lineage. EvoDevo 2022; 13:17. [PMID: 36123753 PMCID: PMC9484238 DOI: 10.1186/s13227-022-00202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopod T. transversa. RESULTS Transcriptome and genome searches for the 10 target genes in the brachiopods Terebratalia transversa, Lingula anatina, Novocrania anomala, the bryozoans Bugula neritina and Membranipora membranacea, and the phoronids Phoronis australis and Phoronopsis harmeri resulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception in L. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genes engrailed, distal-less, ferritin, perlucin, sp1 and sp2 were shown to be expressed in the biomineralising mantle margin of T. transversa juveniles. CONCLUSIONS The gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid-bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.
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18
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Khalturin K, Shunatova N, Shchenkov S, Sasakura Y, Kawamitsu M, Satoh N. Polyzoa is back: The effect of complete gene sets on the placement of Ectoprocta and Entoprocta. SCIENCE ADVANCES 2022; 8:eabo4400. [PMID: 35776797 PMCID: PMC10883361 DOI: 10.1126/sciadv.abo4400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The phylogenomic approach has largely resolved metazoan phylogeny and improved our knowledge of animal evolution based on morphology, paleontology, and embryology. Nevertheless, the placement of two major lophotrochozoan phyla, Entoprocta (Kamptozoa) and Ectoprocta (Bryozoa), remains highly controversial: Originally considered as a single group named Polyzoa (Bryozoa), they were separated on the basis of morphology. So far, each new study of lophotrochozoan evolution has still consistently proposed different phylogenetic positions for these groups. Here, we reinvestigated the placement of Entoprocta and Ectoprocta using highly complete datasets with rigorous contamination removal. Our results from maximum likelihood, Bayesian, and coalescent analyses strongly support the topology in which Entoprocta and Bryozoa form a distinct clade, placed as a sister group to all other lophotrochozoan clades: Annelida, Mollusca, Brachiopoda, Phoronida, and Nemertea. Our study favors the evolutionary scenario where Entoprocta, Cycliophora, and Bryozoa constitute one of the earliest branches among Lophotrochozoa and thus supports the Polyzoa hypothesis.
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Affiliation(s)
- Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Natalia Shunatova
- Department of Invertebrate Zoology, St. Petersburg State University, Saint-Petersburg, Russia
| | - Sergei Shchenkov
- Department of Invertebrate Zoology, St. Petersburg State University, Saint-Petersburg, Russia
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka 415-0025, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
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19
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Uribe JE, González VL, Irisarri I, Kano Y, Herbert DG, Strong EE, Harasewych MG. A phylogenomic backbone for gastropod molluscs. Syst Biol 2022; 71:1271-1280. [PMID: 35766870 DOI: 10.1093/sysbio/syac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Gastropods have survived several mass extinctions during their evolutionary history resulting in extraordinary diversity in morphology, ecology, and developmental modes, which complicate the reconstruction of a robust phylogeny. Currently, gastropods are divided into six subclasses: Caenogastropoda, Heterobranchia, Neomphaliones, Neritimorpha, Patellogastropoda, and Vetigastropoda. Phylogenetic relationships among these taxa historically lack consensus, despite numerous efforts using morphological and molecular information. We generated sequence data for transcriptomes derived from twelve taxa belonging to clades with little or no prior representation in previous studies in order to infer the deeper cladogenetic events within Gastropoda and, for the first time, infer the position of the deep-sea Neomphaliones using a phylogenomic approach. We explored the impact of missing data, homoplasy, and compositional heterogeneity on the inferred phylogenetic hypotheses. We recovered a highly supported backbone for gastropod relationships that is congruent with morphological and mitogenomic evidence, in which Patellogastropoda, true limpets, are the sister lineage to all other gastropods (Orthogastropoda) which are divided into two main clades (i) Vetigastropoda s.l. (including Pleurotomariida + Neomphaliones) and (ii) Neritimorpha + (Caenogastropoda + Heterobranchia). As such, our results support the recognition of five subclasses (or infraclasses) in Gastropoda: Patellogastropoda, Vetigastropoda, Neritimorpha, Caenogastropoda and Heterobranchia.
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Affiliation(s)
- Juan E Uribe
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - Vanessa L González
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany.,Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Museum Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Yasunori Kano
- Department of Marine Ecosystems Dynamics, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - David G Herbert
- Department of Natural Sciences, National Museum Wales, Cathays Park, Cardiff, CF10 3NP, UK
| | - Ellen E Strong
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
| | - M G Harasewych
- Department of Invertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, P O Box 37012 Washington, DC 20013-7012, USA
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20
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Multigenerational laboratory culture of pelagic ctenophores and CRISPR-Cas9 genome editing in the lobate Mnemiopsis leidyi. Nat Protoc 2022; 17:1868-1900. [PMID: 35697825 DOI: 10.1038/s41596-022-00702-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
Despite long-standing experimental interest in ctenophores due to their unique biology, ecological influence and evolutionary status, previous work has largely been constrained by the periodic seasonal availability of wild-caught animals and difficulty in reliably closing the life cycle. To address this problem, we have developed straightforward protocols that can be easily implemented to establish long-term multigenerational cultures for biological experimentation in the laboratory. In this protocol, we describe the continuous culture of the Atlantic lobate ctenophore Mnemiopsis leidyi. A rapid 3-week egg-to-egg generation time makes Mnemiopsis suitable for a wide range of experimental genetic, cellular, embryological, physiological, developmental, ecological and evolutionary studies. We provide recommendations for general husbandry to close the life cycle of Mnemiopsis in the laboratory, including feeding requirements, light-induced spawning, collection of embryos and rearing of juveniles to adults. These protocols have been successfully applied to maintain long-term multigenerational cultures of several species of pelagic ctenophores, and can be utilized by laboratories lacking easy access to the ocean. We also provide protocols for targeted genome editing via microinjection with CRISPR-Cas9 that can be completed within ~2 weeks, including single-guide RNA synthesis, early embryo microinjection, phenotype assessment and sequence validation of genome edits. These protocols provide a foundation for using Mnemiopsis as a model organism for functional genomic analyses in ctenophores.
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21
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Reddien PW. Positional Information and Stem Cells Combine to Result in Planarian Regeneration. Cold Spring Harb Perspect Biol 2022; 14:a040717. [PMID: 34518341 PMCID: PMC9121904 DOI: 10.1101/cshperspect.a040717] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The capacity for regeneration is broad in the animal kingdom. Planarians are flatworms that can regenerate any missing body part and their regenerative powers have combined with ease of experimentation to make them a classic regeneration model for more than a century. Pluripotent stem cells called neoblasts generate missing planarian tissues. Fate specification happens in the neoblasts, and this can occur in response to regeneration instructions in the form of positional information. Fate specification can lead to differentiating cells in single steps rather than requiring a long lineage hierarchy. Planarians display constitutive expression of positional information from muscle cells, which is required for patterned maintenance of tissues in tissue turnover. Amputation leads to the rapid resetting of positional information in a process triggered by wound signaling and the resetting of positional information is required for regeneration. These findings suggest a model for planarian regeneration in which adult positional information resets after injury to regulate stem cells to bring about the replacement of missing parts.
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Affiliation(s)
- Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
- Department of Biology, MIT, Cambridge, Massachusetts 02139, USA
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22
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Ctenophores are direct developers that reproduce continuously beginning very early after hatching. Proc Natl Acad Sci U S A 2022; 119:e2122052119. [PMID: 35476523 PMCID: PMC9170174 DOI: 10.1073/pnas.2122052119] [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] [Indexed: 12/21/2022] Open
Abstract
A substantial body of literature reports that ctenophores exhibit an apparently unique life history characterized by biphasic sexual reproduction, the first phase of which is called larval reproduction or dissogeny. Whether this strategy is plastically deployed or a typical part of these species’ life history was unknown. In contrast to previous reports, we show that the ctenophore Mnemiopsis leidyi does not have separate phases of early and adult reproduction, regardless of the morphological transition to what has been considered the adult form. Rather, these ctenophores begin to reproduce at a small body size and spawn continuously from this point onward under adequate environmental conditions. They do not display a gap in productivity for metamorphosis or other physiological transition at a certain body size. Furthermore, nutritional and environmental constraints on fecundity are similar in both small and large animals. Our results provide critical parameters for understanding resource partitioning between growth and reproduction in this taxon, with implications for management of this species in its invaded range. Finally, we report an observation of similarly small-size spawning in a beroid ctenophore, which is morphologically, ecologically, and phylogenetically distinct from other ctenophores reported to spawn at small sizes. We conclude that spawning at small body size should be considered as the default, on-time developmental trajectory rather than as precocious, stress-induced, or otherwise unusual for ctenophores. The ancestral ctenophore was likely a direct developer, consistent with the hypothesis that multiphasic life cycles were introduced after the divergence of the ctenophore lineage.
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23
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Willson J, Roddur MS, Liu B, Zaharias P, Warnow T. DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition. Syst Biol 2022; 71:610-629. [PMID: 34450658 PMCID: PMC9016570 DOI: 10.1093/sysbio/syab070] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 11/21/2022] Open
Abstract
Species tree inference from gene family trees is a significant problem in computational biology. However, gene tree heterogeneity, which can be caused by several factors including gene duplication and loss, makes the estimation of species trees very challenging. While there have been several species tree estimation methods introduced in recent years to specifically address gene tree heterogeneity due to gene duplication and loss (such as DupTree, FastMulRFS, ASTRAL-Pro, and SpeciesRax), many incur high cost in terms of both running time and memory. We introduce a new approach, DISCO, that decomposes the multi-copy gene family trees into many single copy trees, which allows for methods previously designed for species tree inference in a single copy gene tree context to be used. We prove that using DISCO with ASTRAL (i.e., ASTRAL-DISCO) is statistically consistent under the GDL model, provided that ASTRAL-Pro correctly roots and tags each gene family tree. We evaluate DISCO paired with different methods for estimating species trees from single copy genes (e.g., ASTRAL, ASTRID, and IQ-TREE) under a wide range of model conditions, and establish that high accuracy can be obtained even when ASTRAL-Pro is not able to correctly roots and tags the gene family trees. We also compare results using MI, an alternative decomposition strategy from Yang Y. and Smith S.A. (2014), and find that DISCO provides better accuracy, most likely as a result of covering more of the gene family tree leafset in the output decomposition. [Concatenation analysis; gene duplication and loss; species tree inference; summary method.].
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Affiliation(s)
- James Willson
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinmoy Saha Roddur
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Baqiao Liu
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paul Zaharias
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tandy Warnow
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Srivastava M. Studying development, regeneration, stem cells, and more in the acoel Hofstenia miamia. Curr Top Dev Biol 2022; 147:153-172. [PMID: 35337448 DOI: 10.1016/bs.ctdb.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Acoel worms represent an enigmatic lineage of animals (Acoelomorpha) that has danced around the tree of animal life. Morphology-based classification placed them as flatworms (Phylum Platyhelminthes), with much of their biology being interpreted as a variation on what is observed in better-studied members of that phylum. However, molecular phylogenies suggest that acoels belong to a clade (Xenacoelomorpha) that could be a sister group to other animals with bilateral symmetry (Bilateria) or could belong within deuterostomes, closely related to a group that includes sea stars (Ambulacraria). This change in phylogenetic position has led to renewed interest in the biology of acoels, which can now offer insights into the evolution of many bilaterian traits. The acoel Hofstenia miamia has emerged as a powerful new research organism that enables mechanistic studies of xenacoelomorph biology, especially of developmental and regenerative processes. This article explains the motivation for developing Hofstenia as a new model system, describes Hofstenia biology, highlights the tools and resources that make Hofstenia a good research organism, and considers the questions that Hofstenia is well-positioned to answer. Finally, looking to the future, this article serves as an invitation to new and established scientists to join the growing community of researchers studying this exciting model system.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States.
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25
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Martindale MQ. Emerging models: The "development" of the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis as useful experimental models. Curr Top Dev Biol 2022; 147:93-120. [PMID: 35337468 DOI: 10.1016/bs.ctdb.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The goal of this chapter is to explain the reasoning for developing two understudied invertebrate animal species for asking specific biological questions. The first is the ctenophore (comb jelly) Mnemiopsis leidyi and the second is the anthozoan cnidarian (starlet sea anemone) Nematostella vectensis. Although these two taxa belong to some of the earliest branching extant metazoan clades, their developmental features could hardly be more different from one another. This should serve as a general warning to be careful when extrapolating comparisons of one species to another. Two-taxon comparisons are especially flawed; and to interpret features in a phylogenetic context one must sample carefully within a given taxon to determine how representative certain features are before comparing with other clades. The other benefit of this comparison is to identify key practical factors when attempting to develop new species for experimental investigation.
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Affiliation(s)
- Mark Q Martindale
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, United States.
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26
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Ahmed M, Roberts NG, Adediran F, Smythe AB, Kocot KM, Holovachov O. Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.769565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.
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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] [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. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01196-w.
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Asai M, Miyazawa H, Yanase R, Inaba K, Nakano H. A New Species of Acoela Possessing a Middorsal Appendage with a Possible Sensory Function. Zoolog Sci 2022; 39:147-156. [DOI: 10.2108/zs210058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Masashi Asai
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Hideyuki Miyazawa
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Ryuji Yanase
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
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Ozment E, Tamvacakis AN, Zhou J, Rosiles-Loeza PY, Escobar-Hernandez EE, Fernandez-Valverde SL, Nakanishi N. Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity. eLife 2021; 10:74336. [PMID: 34939935 PMCID: PMC8846589 DOI: 10.7554/elife.74336] [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: 09/30/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Although specialized mechanosensory cells are found across animal phylogeny, early evolutionary histories of mechanoreceptor development remain enigmatic. Cnidaria (e.g. sea anemones and jellyfishes) is the sister group to well-studied Bilateria (e.g. flies and vertebrates), and has two mechanosensory cell types – a lineage-specific sensory effector known as the cnidocyte, and a classical mechanosensory neuron referred to as the hair cell. While developmental genetics of cnidocytes is increasingly understood, genes essential for cnidarian hair cell development are unknown. Here, we show that the class IV POU homeodomain transcription factor (POU-IV) – an indispensable regulator of mechanosensory cell differentiation in Bilateria and cnidocyte differentiation in Cnidaria – controls hair cell development in the sea anemone cnidarian Nematostella vectensis. N. vectensis POU-IV is postmitotically expressed in tentacular hair cells, and is necessary for development of the apical mechanosensory apparatus, but not of neurites, in hair cells. Moreover, it binds to deeply conserved DNA recognition elements, and turns on a unique set of effector genes – including the transmembrane receptor-encoding gene polycystin 1 – specifically in hair cells. Our results suggest that POU-IV directs differentiation of cnidarian hair cells and cnidocytes via distinct gene regulatory mechanisms, and support an evolutionarily ancient role for POU-IV in defining the mature state of mechanosensory neurons.
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Affiliation(s)
- Ethan Ozment
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Arianna N Tamvacakis
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Pablo Yamild Rosiles-Loeza
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | | | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Nagayasu Nakanishi
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
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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: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [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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31
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Presnell JS, Browne WE. Krüppel-like factor gene function in the ctenophore Mnemiopsis leidyi assessed by CRISPR/Cas9-mediated genome editing. Development 2021; 148:272041. [PMID: 34373891 DOI: 10.1242/dev.199771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/26/2021] [Indexed: 12/21/2022]
Abstract
The Krüppel-like factor (Klf) gene family encodes transcription factors that play an important role in the regulation of stem cell proliferation, cell differentiation and development in bilaterians. Although Klf genes have been shown to specify functionally various cell types in non-bilaterian animals, their role in early-diverging animal lineages has not been assessed. Thus, the ancestral activity of these transcription factors in animal development is not well understood. The ctenophore Mnemiopsis leidyi has emerged as an important non-bilaterian model system for understanding early animal evolution. Here, we characterize the expression and functional role of Klf genes during M. leidyi embryogenesis. Zygotic Klf gene function was assessed with both CRISPR/Cas9-mediated genome editing and splice-blocking morpholino oligonucleotide knockdown approaches. Abrogation of zygotic Klf expression during M. leidyi embryogenesis resulted in abnormal development of several organs, including the pharynx, tentacle bulbs and apical organ. Our data suggest an ancient role for Klf genes in regulating endodermal patterning, possibly through regulation of cell proliferation.
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Affiliation(s)
- Jason S Presnell
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
| | - William E Browne
- Department of Biology, University of Miami, Cox Science Center, 1301 Memorial Drive, Miami, FL 33146, USA
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Gąsiorowski L, Børve A, Cherneva IA, Orús-Alcalde A, Hejnol A. Molecular and morphological analysis of the developing nemertean brain indicates convergent evolution of complex brains in Spiralia. BMC Biol 2021; 19:175. [PMID: 34452633 PMCID: PMC8400761 DOI: 10.1186/s12915-021-01113-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/30/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The brain anatomy in the clade Spiralia can vary from simple, commissural brains (e.g., gastrotrichs, rotifers) to rather complex, partitioned structures (e.g., in cephalopods and annelids). How often and in which lineages complex brains evolved still remains unclear. Nemerteans are a clade of worm-like spiralians, which possess a complex central nervous system (CNS) with a prominent brain, and elaborated chemosensory and neuroglandular cerebral organs, which have been previously suggested as homologs to the annelid mushroom bodies. To understand the developmental and evolutionary origins of the complex brain in nemerteans and spiralians in general, we investigated details of the neuroanatomy and gene expression in the brain and cerebral organs of the juveniles of nemertean Lineus ruber. RESULTS In the juveniles, the CNS is already composed of all major elements present in the adults, including the brain, paired longitudinal lateral nerve cords, and an unpaired dorsal nerve cord, which suggests that further neural development is mostly related with increase in the size but not in complexity. The ultrastructure of the juvenile cerebral organ revealed that it is composed of several distinct cell types present also in the adults. The 12 transcription factors commonly used as brain cell type markers in bilaterians show region-specific expression in the nemertean brain and divide the entire organ into several molecularly distinct areas, partially overlapping with the morphological compartments. Additionally, several of the mushroom body-specific genes are expressed in the developing cerebral organs. CONCLUSIONS The dissimilar expression of molecular brain markers between L. ruber and the annelid Platynereis dumerilii indicates that the complex brains present in those two species evolved convergently by independent expansions of non-homologous regions of a simpler brain present in their last common ancestor. Although the same genes are expressed in mushroom bodies and cerebral organs, their spatial expression within organs shows apparent differences between annelids and nemerteans, indicating convergent recruitment of the same genes into patterning of non-homologous organs or hint toward a more complicated evolutionary process, in which conserved and novel cell types contribute to the non-homologous structures.
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Affiliation(s)
| | - Aina Børve
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Irina A Cherneva
- Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Andreas Hejnol
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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The Natterin Proteins Diversity: A Review on Phylogeny, Structure, and Immune Function. Toxins (Basel) 2021; 13:toxins13080538. [PMID: 34437409 PMCID: PMC8402412 DOI: 10.3390/toxins13080538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Since the first record of the five founder members of the group of Natterin proteins in the venom of the medically significant fish Thalassophryne nattereri, new sequences have been identified in other species. In this work, we performed a detailed screening using available genome databases across a wide range of species to identify sequence members of the Natterin group, sequence similarities, conserved domains, and evolutionary relationships. The high-throughput tools have enabled us to dramatically expand the number of members within this group of proteins, which has a remote origin (around 400 million years ago) and is spread across Eukarya organisms, even in plants and primitive Agnathans jawless fish. Overall, the survey resulted in 331 species presenting Natterin-like proteins, mainly fish, and 859 putative genes. Besides fish, the groups with more species included in our analysis were insects and birds. The number and variety of annotations increased the knowledge of the obtained sequences in detail, such as the conserved motif AGIP in the pore-forming loop involved in the transmembrane barrel insertion, allowing us to classify them as important constituents of the innate immune defense system as effector molecules activating immune cells by interacting with conserved intracellular signaling mechanisms in the hosts.
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34
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Kimura JO, Ricci L, Srivastava M. Embryonic development in the acoel Hofstenia miamia. Development 2021; 148:270768. [PMID: 34196362 DOI: 10.1242/dev.188656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/20/2021] [Indexed: 01/03/2023]
Abstract
Acoels are marine worms that belong to the phylum Xenacoelomorpha, a deep-diverging bilaterian lineage. This makes acoels an attractive system for studying the evolution of major bilaterian traits. Thus far, acoel development has not been described in detail at the morphological and transcriptomic levels in a species in which functional genetic studies are possible. We present a set of developmental landmarks for embryogenesis in the highly regenerative acoel Hofstenia miamia. We generated a developmental staging atlas from zygote to hatched worm based on gross morphology, with accompanying bulk transcriptome data. Hofstenia embryos undergo a stereotyped cleavage program known as duet cleavage, which results in two large vegetal pole 'macromeres' and numerous small animal pole 'micromeres'. These macromeres become internalized as micromere progeny proliferate and move vegetally. We also noted a second, previously undescribed, cell-internalization event at the animal pole, following which we detected major body axes and tissues corresponding to all three germ layers. Our work on Hofstenia embryos provides a resource for mechanistic investigations of acoel development, which will yield insights into the evolution of bilaterian development and regeneration.
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Affiliation(s)
- Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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von Döhren J. Diversity in the Development of the Neuromuscular System of Nemertean Larvae (Nemertea, Spiralia). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.654846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In studies on the development of nervous systems and musculature, fluorescent labeling of neuroactive substances and filamentous actin (f-actin) of muscle cells and the subsequent analysis with confocal laser scanning microscopy (CLSM), has led to a broad comparative data set for the majority of the clades of the superphylum Spiralia. However, a number of clades remain understudied, which results in gaps in our knowledge that drastically hamper the formulation of broad-scale hypotheses on the evolutionary developmental biology (EvoDevo) of the structures in question. Regarding comparative data on the development of the peptidergic nervous system and the musculature of species belonging to the spiralian clade Nemertea (ribbon worms), such considerable knowledge gaps are manifest. This paper presents first findings on fluorescent labeling of the FMRFamide-like component of the nervous system and contributes additional data on the muscle development in the presently still underrepresented larvae of palaeo- and hoplonemertean species. Whereas the architecture of the FMRFamide-like nervous system is comparably uniform between the studied representatives, the formation of the musculature differs considerably, exhibiting developmental modes yet undescribed for any spiralian species. The presented results fill a significant gap in the spiralian EvoDevo data set and thus allow for further elaboration of hypotheses on the ancestral pattern of the musculature and a prominent component of the nervous system in Nemertea. However, with respect to the variety observed, it is expected that the true diversity of the developmental pathways is still to be discovered when more detailed data on other nemertean species will be available.
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The Roles of Protein Structure, Taxon Sampling, and Model Complexity in Phylogenomics: A Case Study Focused on Early Animal Divergences. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1020008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite the long history of using protein sequences to infer the tree of life, the potential for different parts of protein structures to retain historical signal remains unclear. We propose that it might be possible to improve analyses of phylogenomic datasets by incorporating information about protein structure. We test this idea using the position of the root of Metazoa (animals) as a model system. We examined the distribution of “strongly decisive” sites (alignment positions that support a specific tree topology) in a dataset comprising >1500 proteins and almost 100 taxa. The proportion of each class of strongly decisive sites in different structural environments was very sensitive to the model used to analyze the data when a limited number of taxa were used but they were stable when taxa were added. As long as enough taxa were analyzed, sites in all structural environments supported the same topology regardless of whether standard tree searches or decisive sites were used to select the optimal tree. However, the use of decisive sites revealed a difference between the support for minority topologies for sites in different structural environments: buried sites and sites in sheet and coil environments exhibited equal support for the minority topologies, whereas solvent-exposed and helix sites had unequal numbers of sites, supporting the minority topologies. This suggests that the relatively slowly evolving buried, sheet, and coil sites are giving an accurate picture of the true species tree and the amount of conflict among gene trees. Taken as a whole, this study indicates that phylogenetic analyses using sites in different structural environments can yield different topologies for the deepest branches in the animal tree of life and that analyzing larger numbers of taxa eliminates this conflict. More broadly, our results highlight the desirability of incorporating information about protein structure into phylogenomic analyses.
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Isaeva MA, Kosevich IA, Temereva EN. Peculiarities of Tentacle Innervation of Flustrellidra hispida and Evolution of Lophophore in Bryozoa. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2021; 496:30-33. [PMID: 33635487 DOI: 10.1134/s0012496621010038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022]
Abstract
The study of the lophophore organization is of great importance for the reconstruction of lophophorate phylogeny and for understanding the evolutionary transformation in each phylum of Lophophorata. The innervation of the lophophore in ctenostome bryozoan Flustrellidra hispida was studied using immunocytochemistry and confocal laser scanning microscopy. It has been demonstrated that this species has an outer nerve ring giving rise to the tentacle nerves. The outer nerve ring was earlier described in some ctenostomates and cyclostomates, but not as connected with nerves. The discovered feature of lophophore innervation in F. hispida suggests the evolutionary transformation from a hypothetical phoronida-like ancestor lophophore bearing a prominent outer nerve ring with numerous tentacle nerves emanating from it, to the complex bell-shaped lophophore of F. hispida with a well-pronounced outer nervous ring bearing a few tentacle nerves. The next one in this hypothetical row is the lophophore of the other ctenostomates and some cyclostomates with no ring-nerve connection and cheilostomates lophophore with no outer nerve ring at all.
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Affiliation(s)
- M A Isaeva
- Moscow State University, 119991, Moscow, Russia
| | | | - E N Temereva
- Moscow State University, 119991, Moscow, Russia.
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Praher D, Zimmermann B, Dnyansagar R, Miller DJ, Moya A, Modepalli V, Fridrich A, Sher D, Friis-Møller L, Sundberg P, Fôret S, Ashby R, Moran Y, Technau U. Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proc Biol Sci 2021; 288:20203169. [PMID: 33622129 PMCID: PMC7935066 DOI: 10.1098/rspb.2020.3169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.
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Affiliation(s)
- Daniela Praher
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - David J. Miller
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, UK
| | - Arie Fridrich
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Lene Friis-Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Lyngby, Denmark
| | - Per Sundberg
- Department of Zoology, University of Gothenburg, Gothenburg, Sweden
| | - Sylvain Fôret
- Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia
| | - Regan Ashby
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
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39
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Kutyumov VA, Predeus AV, Starunov VV, Maltseva AL, Ostrovsky AN. Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features. Mitochondrion 2021; 59:96-104. [PMID: 33631347 DOI: 10.1016/j.mito.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.
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Affiliation(s)
- Vladimir A Kutyumov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia.
| | - Alexander V Predeus
- Bioinformatics Institute, Kantemirovskaya 2A, 197342 Saint Petersburg, Russia
| | - Viktor V Starunov
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Arina L Maltseva
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia
| | - Andrew N Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; Department of Palaeontology, Faculty of Geography, Geology and Astronomy, University of Vienna, Althanstr. 14, 1090 Vienna, Austria.
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40
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Abstract
Hemichordates, along with echinoderms and chordates, belong to the lineage of bilaterians called the deuterostomes. Their phylogenetic position as an outgroup to chordates provides an opportunity to investigate the evolutionary origins of the chordate body plan and reconstruct ancestral deuterostome characters. The body plans of the hemichordates and chordates are organizationally divergent making anatomical comparisons very challenging. The developmental underpinnings of animal body plans are often more conservative than the body plans they regulate, and offer a novel data set for making comparisons between morphologically divergent body architectures. Here I review the hemichordate developmental data generated over the past 20 years that further test hypotheses of proposed morphological affinities between the two taxa, but also compare the conserved anteroposterior, dorsoventral axial patterning programs and germ layer specification programs. These data provide an opportunity to determine which developmental programs are ancestral deuterostome or bilaterian innovations, and which ones occurred in stem chordates or vertebrates representing developmental novelties of the chordate body plan.
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41
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Kapli P, Telford MJ. Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha. SCIENCE ADVANCES 2020; 6:eabc5162. [PMID: 33310849 PMCID: PMC7732190 DOI: 10.1126/sciadv.abc5162] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/27/2020] [Indexed: 05/21/2023]
Abstract
The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives.
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Affiliation(s)
- Paschalia Kapli
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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42
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Jokura K, Inaba K. Structural diversity and distribution of cilia in the apical sense organ of the ctenophore Bolinopsis mikado. Cytoskeleton (Hoboken) 2020; 77:442-455. [PMID: 33103333 DOI: 10.1002/cm.21640] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 02/03/2023]
Abstract
The apical organ of ctenophores is the center of sensory information that controls locomotion. Previous studies have described several types of cilia in this organ. However, detailed ciliary structures, particularly axonemal structures, have not been extensively investigated. Here, we reported that the apical organ of the ctenophore Bolinopsis mikado contains six types of cilia with different axonemal structures. These include the typical "9 + 2" motile axonemes, with both outer and inner dynein arms, only the inner dynein arm, or no dynein arm; axonemes with electron-dense structures in the A-tubules; "9 + 0" axonemes lacking the central pair of microtubules; and axonemes with compartmenting lamellae. Considering that "9 + 2" axonemal structures with both dynein arms are thought to be ancestral forms of cilia, the apical organ of ctenophores would comprise an elaborate assembly of modified ciliary forms that sense and transmit extracellular stimuli and generate various fluid flows.
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Affiliation(s)
- Kei Jokura
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
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43
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Reverse Genetic Approaches to Investigate the Neurobiology of the Cnidarian Sea Anemone Nematostella vectensis. Methods Mol Biol 2020; 2047:25-43. [PMID: 31552647 DOI: 10.1007/978-1-4939-9732-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The cnidarian sea anemone Nematostella vectensis has grown in popularity as a model system to complement the ongoing work in traditional bilaterian model species (e.g. Drosophila, C. elegans, vertebrate). The driving force behind developing cnidarian model systems is the potential of this group of animals to impact EvoDevo studies aimed at better determining the origin and evolution of bilaterian traits, such as centralized nervous systems. However, it is becoming apparent that cnidarians have the potential to impact our understanding of regenerative neurogenesis and systems neuroscience. Next-generation sequencing and the development of reverse genetic approaches led to functional genetics becoming routine in the Nematostella system. As a result, researchers are beginning to understand how cnidarian nerve nets are related to the bilaterian nervous systems. This chapter describes the methods for morpholino and mRNA injections to knockdown or overexpress genes of interest, respectively. Carrying out these techniques in Nematostella requires obtaining and preparing embryos for microinjection, designing and generating effective morpholino and mRNA molecules with controls for injection, and optimizing injection conditions.
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44
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Novel data on the innervation of the lophophore in adult phoronids (Lophophorata, Phoronida). ZOOLOGY 2020; 143:125832. [PMID: 32971479 DOI: 10.1016/j.zool.2020.125832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 11/21/2022]
Abstract
The structure of the lophophore nervous system may help clarify the status of the clade Lophophorata, whose monophyly is debated. In the current study, antibody labeling and confocal laser scanning microscopy revealed previously undescribed main nerve elements in the lophophore in adult phoronids: Phoronis australis and Phoronopsis harmeri. In both species, the nervous system includes a dorsal ganglion, a tentacle nerve ring, an inner nerve ring, intertentacular groups of perikarya, and tentacle nerves. The dorsal ganglion and tentacle nerve ring contain many serotonin-like immunoreactive perikarya of different sizes. The inner nerve ring is described for the first time in adult phoronids with complex lophophore. It contains a thin bundle of serotonin-like immunoreactive neurites. The tentacles possess abfrontal, frontal, and laterofrontal nerves. The abfrontal nerves originate from the tentacle nerve ring; the frontal tentacle nerves extend from the inner nerve ring in P. harmeri and from the intertentacular frontal nerves in P. australis. The intertentacular groups of perikarya are found in phoronids for the first time. These small nerve centers connect with neither the tentacle nerve ring nor the inner nerve ring, giving rise to the laterofrontal tentacle nerves. The discovery of the inner nerve ring in adult phoronids makes the architecture of the lophophore nervous system similar in all lophophorates and thereby supports the monophyly of this group. The presence of intertentacular nerves, perikarya, and groups of perikarya is a typical feature of the nervous system in lophophorate presumably coordinating movements of the tentacles and thereby increasing the efficiency of lophophore functioning.
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45
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Salinas-Saavedra M, Martindale MQ. Par protein localization during the early development of Mnemiopsis leidyi suggests different modes of epithelial organization in the metazoa. eLife 2020; 9:54927. [PMID: 32716297 PMCID: PMC7441587 DOI: 10.7554/elife.54927] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
In bilaterians and cnidarians, epithelial cell-polarity is regulated by the interactions between Par proteins, Wnt/PCP signaling pathway, and cell-cell adhesion. Par proteins are highly conserved across Metazoa, including ctenophores. But strikingly, ctenophore genomes lack components of the Wnt/PCP pathway and cell-cell adhesion complexes raising the question if ctenophore cells are polarized by mechanisms involving Par proteins. Here, by using immunohistochemistry and live-cell imaging of specific mRNAs, we describe for the first time the subcellular localization of selected Par proteins in blastomeres and epithelial cells during the embryogenesis of the ctenophore Mnemiopsis leidyi. We show that these proteins distribute differently compared to what has been described for other animals, even though they segregate in a host-specific fashion when expressed in cnidarian embryos. This differential localization might be related to the emergence of different junctional complexes during metazoan evolution.
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Affiliation(s)
- Miguel Salinas-Saavedra
- The Whitney Laboratory for Marine Bioscience, and the Department of Biology, University of Florida, St. Augustine, United States
| | - Mark Q Martindale
- The Whitney Laboratory for Marine Bioscience, and the Department of Biology, University of Florida, St. Augustine, United States
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46
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Hulett RE, Potter D, Srivastava M. Neural architecture and regeneration in the acoel Hofstenia miamia. Proc Biol Sci 2020; 287:20201198. [PMID: 32693729 PMCID: PMC7423668 DOI: 10.1098/rspb.2020.1198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The origin of bilateral symmetry, a major transition in animal evolution, coincided with the evolution of organized nervous systems that show regionalization along major body axes. Studies of Xenacoelomorpha, the likely outgroup lineage to all other animals with bilateral symmetry, can inform the evolutionary history of animal nervous systems. Here, we characterized the neural anatomy of the acoel Hofstenia miamia. Our analysis of transcriptomic data uncovered orthologues of enzymes for all major neurotransmitter synthesis pathways. Expression patterns of these enzymes revealed the presence of a nerve net and an anterior condensation of neural cells. The anterior condensation was layered, containing several cell types with distinct molecular identities organized in spatially distinct territories. Using these anterior cell types and structures as landmarks, we obtained a detailed timeline for regeneration of the H. miamia nervous system, showing that the anterior condensation is restored by eight days after amputation. Our work detailing neural anatomy in H. miamia will enable mechanistic studies of neural cell type diversity and regeneration and provide insight into the evolution of these processes.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Deirdre Potter
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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47
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Heger P, Zheng W, Rottmann A, Panfilio KA, Wiehe T. The genetic factors of bilaterian evolution. eLife 2020; 9:e45530. [PMID: 32672535 PMCID: PMC7535936 DOI: 10.7554/elife.45530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
The Cambrian explosion was a unique animal radiation ~540 million years ago that produced the full range of body plans across bilaterians. The genetic mechanisms underlying these events are unknown, leaving a fundamental question in evolutionary biology unanswered. Using large-scale comparative genomics and advanced orthology evaluation techniques, we identified 157 bilaterian-specific genes. They include the entire Nodal pathway, a key regulator of mesoderm development and left-right axis specification; components for nervous system development, including a suite of G-protein-coupled receptors that control physiology and behaviour, the Robo-Slit midline repulsion system, and the neurotrophin signalling system; a high number of zinc finger transcription factors; and novel factors that previously escaped attention. Contradicting the current view, our study reveals that genes with bilaterian origin are robustly associated with key features in extant bilaterians, suggesting a causal relationship.
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Affiliation(s)
- Peter Heger
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Wen Zheng
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Anna Rottmann
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, Cologne Biocenter, University of CologneCologneGermany
- School of Life Sciences, University of Warwick, Gibbet Hill CampusCoventryUnited Kingdom
| | - Thomas Wiehe
- Institute for Genetics, Cologne Biocenter, University of CologneCologneGermany
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48
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Curini-Galletti M, Artois T, Di Domenico M, Fontaneto D, Jondelius U, Jörger KM, Leasi F, Martínez A, Norenburg JL, Sterrer W, Todaro MA. Contribution of soft-bodied meiofaunal taxa to Italian marine biodiversity. THE EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1786607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- M. Curini-Galletti
- Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - T. Artois
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - M. Di Domenico
- Center for Marine Studies, Universidade Federal do Paraná, Curitiba, Brazil
| | - D. Fontaneto
- Molecular Ecology Group, Water Research Institute - CNR, Verbania, Italy
| | - U. Jondelius
- Department of Invertebrate Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - K. M. Jörger
- SNSB-Bavarian State Collection of Zoology, Munich, Germany
| | - F. Leasi
- Department of Biology, Geology and Environmental Science, University of Tennessee, Chattanooga, TN, USA
| | - A. Martínez
- Molecular Ecology Group, Water Research Institute - CNR, Verbania, Italy
| | - J. L. Norenburg
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution (USA), Washington, DC, USA
| | | | - M. A. Todaro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Modena, Italy
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49
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Santagata S. Genes with evidence of positive selection as potentially related to coloniality and the evolution of morphological features among the lophophorates and entoprocts. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:267-280. [PMID: 32638536 DOI: 10.1002/jez.b.22975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 05/14/2020] [Accepted: 06/03/2020] [Indexed: 02/06/2023]
Abstract
Evolutionary mechanisms that underlie the origins of coloniality among organisms are diverse. Some animal colonies may be comprised strictly of clonal individuals formed from asexual budding or comprised of a chimera of clonal and sexually produced individuals that fuse secondarily. This investigation focuses on select members of the lophophorates and entoprocts whose evolutionary relationships remain enigmatic even in the age of genomics. Using transcriptomic data sets, two coloniality-based hypotheses are tested in a phylogenetic context to find candidate genes showing evidence of positive selection and potentially convergent molecular signatures among solitary species and taxa-forming colonies from aggregate groups or clonal budding. Approximately 22% of the 387 orthogroups tested showed evidence of positive selection in at least one of the three branch-site tests (CODEML, BUSTED, and aBSREL). Only 12 genes could be reliably associated with a developmental function related to traits linked with coloniality, neuroanatomy, or ciliary fields. Genes testing for both positive selection and convergent molecular characters include orthologues of Radial spoke head, Elongation translation initiation factors, SEC13, and Immediate early response gene5. Maximum likelihood analyses included here resulted in tree topologies typical of other phylogenetic investigations based on wider genomic information. Further genomic and experimental evidence will be needed to resolve whether a solitary ancestor with multiciliated cells that formed aggregate groups gave rise to colonial forms in bryozoans (and perhaps the entoprocts) or that the morphological differences exhibited by phoronids and brachiopods represent trait modifications from a colonial ancestor.
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Affiliation(s)
- Scott Santagata
- Department of Biological and Environmental Sciences, Long Island University, Greenvale, New York
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50
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Arenas Gómez CM, Sabin KZ, Echeverri K. Wound healing across the animal kingdom: Crosstalk between the immune system and the extracellular matrix. Dev Dyn 2020; 249:834-846. [PMID: 32314465 PMCID: PMC7383677 DOI: 10.1002/dvdy.178] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/11/2020] [Indexed: 12/11/2022] Open
Abstract
Tissue regeneration is widespread in the animal kingdom. To date, key roles for different molecular and cellular programs in regeneration have been described, but the ultimate blueprint for this talent remains elusive. In animals capable of tissue regeneration, one of the most crucial stages is wound healing, whose main goal is to close the wound and prevent infection. In this stage, it is necessary to avoid scar formation to facilitate the activation of the immune system and remodeling of the extracellular matrix, key factors in promoting tissue regeneration. In this review, we will discuss the current state of knowledge regarding the role of the immune system and the interplay with the extracellular matrix to trigger a regenerative response.
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Affiliation(s)
- Claudia M. Arenas Gómez
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Keith Z. Sabin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Karen Echeverri
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
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