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Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
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Mańko MK, Munro C, Leclère L. Establishing Bilateral Symmetry in Hydrozoan Planula Larvae, a Review of Siphonophore Early Development. Integr Comp Biol 2023; 63:975-989. [PMID: 37353930 DOI: 10.1093/icb/icad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/02/2023] [Accepted: 06/11/2023] [Indexed: 06/25/2023] Open
Abstract
Siphonophores are colonial hydrozoans, characterized by complex colony organization and unparalleled zooid functional specialization. Recent genomic studies have offered an evolutionary perspective on how this morphological complexity arose, but a molecular characterization of symmetry breaking in siphonophore embryonic development is still largely missing. Here, bringing together historical data on early development with new immunohistochemical data, we review the diversity of developmental trajectories that lead to the formation of bilaterally symmetric planula larvae in siphonophores. Embryonic development, up to the planula stage, is remarkably similar across siphonophore phylogeny. Then, with the appearance of the lateral endodermal thickening (= ventral endoderm), larval development diverges between taxa, differing in the location and patterning of the primary buds, chronology of budding, establishment of growth zones, and retention of larval zooids. Our work also uncovers a number of open questions in siphonophore development, including homology of different zooids, mechanisms underlying formation and maintenance of spatially restricted growth zone(s), and molecular factors establishing a secondary dorsal-ventral axis in planulae. By discussing siphonophore development and body axes within the broader cnidarian context, we then set the framework for future work on siphonophores, which is finally achievable with the advent of culturing methods.
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Affiliation(s)
- Maciej K Mańko
- Laboratory of Plankton Biology, Department of Marine Biology and Biotechnology, University of Gdańsk, Gdynia, 81-378, Poland
| | - Catriona Munro
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, 75005, France
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-Mer, 06230, France
| | - Lucas Leclère
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-Mer, 06230, France
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Banyuls-sur-Mer, 66650, France
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Damian-Serrano A, Haddock SHD, Dunn CW. The Evolutionary History of Siphonophore Tentilla: Novelties, Convergence, and Integration. Integr Org Biol 2021; 3:obab019. [PMID: 34355122 PMCID: PMC8331849 DOI: 10.1093/iob/obab019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Synopsis Siphonophores are free-living predatory colonial hydrozoan cnidarians found in every region of the ocean. Siphonophore tentilla (tentacle side branches) are unique biological structures for prey capture, composed of a complex arrangement of cnidocytes (stinging cells) bearing different types of nematocysts (stinging capsules) and auxiliary structures. Tentilla present an extensive morphological and functional diversity across species. While associations between tentillum form and diet have been reported, the evolutionary history giving rise to this morphological diversity is largely unexplored. Here we examine the evolutionary gains and losses of novel tentillum substructures and nematocyst types on the most recent siphonophore phylogeny. Tentilla have a precisely coordinated high-speed strike mechanism of synchronous unwinding and nematocyst discharge. Here we characterize the kinematic diversity of this prey capture reaction using high-speed video and find relationships with morphological characters. Since tentillum discharge occurs in synchrony across a broad morphological diversity, we evaluate how phenotypic integration is maintaining character correlations across evolutionary time. We found that the tentillum morphospace has low dimensionality, identified instances of heterochrony and morphological convergence, and generated hypotheses on the diets of understudied siphonophore species. Our findings indicate that siphonophore tentilla are phenotypically integrated structures with a complex evolutionary history leading to a phylogenetically-structured diversity of forms that are predictive of kinematic performance and feeding habits.
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Affiliation(s)
- A Damian-Serrano
- Osborn Memorial Laboratories, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - S H D Haddock
- Midwater Research, Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039, USA
| | - C W Dunn
- Osborn Memorial Laboratories, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
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Munro C, Vue Z, Behringer RR, Dunn CW. Morphology and development of the Portuguese man of war, Physalia physalis. Sci Rep 2019; 9:15522. [PMID: 31664071 PMCID: PMC6820529 DOI: 10.1038/s41598-019-51842-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/08/2019] [Indexed: 01/31/2023] Open
Abstract
The Portuguese man of war, Physalia physalis, is one of the most conspicuous, but poorly understood members of the pleuston, a community of organisms that occupy a habitat at the sea-air interface. Physalia physalis is a siphonophore that uses a gas-filled float as a sail to catch the wind. The development, morphology, and colony organization of P. physalis is very different from all other siphonophores. Here, we look at live and fixed larval and juvenile specimens, and use optical projection tomography to build on existing knowledge about the morphology and development of this species. We also propose a framework for homologizing the axes with other siphonophores, and also suggest that the tentacle bearing zooids should be called tentacular palpons. Previous descriptions of P. physalis larvae, especially descriptions of budding order, were often framed with the mature colony in mind. However, we use the simpler organization of larvae and the juvenile specimens to inform our understanding of the morphology, budding order, and colony organization in the mature specimen. Finally, we review what is known about the ecology and lifecycle of P. physalis.
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Affiliation(s)
- Catriona Munro
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, 02912, USA.
- Collège de France, Center for Interdisciplinary Research in Biology, 75005, Paris, France.
| | - Zer Vue
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
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Munro C, Siebert S, Zapata F, Howison M, Damian-Serrano A, Church SH, Goetz FE, Pugh PR, Haddock SHD, Dunn CW. Improved phylogenetic resolution within Siphonophora (Cnidaria) with implications for trait evolution. Mol Phylogenet Evol 2018; 127:823-833. [PMID: 29940256 PMCID: PMC6064665 DOI: 10.1016/j.ympev.2018.06.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 05/19/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
Abstract
Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at most depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. They play important roles in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups. There was, however, little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 29 siphonophore species analyzed in combination with 14 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose at least twice.
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Affiliation(s)
- Catriona Munro
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA.
| | - Stefan Siebert
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA; Department of Molecular & Cellular Biology, University of California Davis, Davis, CA 95616, USA(2)
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mark Howison
- Brown Data Science Practice, Brown University, Providence, RI 02912, USA; Watson Institute for International and Public Affairs, Brown University, Providence, RI 02912, USA(2)
| | - Alejandro Damian-Serrano
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Samuel H Church
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA(2)
| | - Freya E Goetz
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA; Smithsonian Institution, National Museum of Natural History, Washington, DC 20560, USA(2)
| | - Philip R Pugh
- National Oceanography Centre, Southampton SO14 3ZH, UK
| | | | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
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Siebert S, Goetz FE, Church SH, Bhattacharyya P, Zapata F, Haddock SHD, Dunn CW. Stem cells in Nanomia bijuga (Siphonophora), a colonial animal with localized growth zones. EvoDevo 2015; 6:22. [PMID: 26090088 PMCID: PMC4471933 DOI: 10.1186/s13227-015-0018-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that are the sites of both elongation and zooid budding. It remained unknown, however, how this unique colony growth and development is realized at the cellular level. RESULTS To understand the colony-level growth and development of siphonophores at the cellular level, we characterize the distribution of proliferating cells and interstitial stem cells (i-cells) in the siphonophore Nanomia bijuga. Within the colony, we find evidence that i-cells are present at the tip of the horn, the structure within the growth zone that gives rise to new zooids. Co-localized gene expression of vasa-1, pl10, piwi, nanos-1, and nanos-2 suggests that i-cells persist in the youngest zooid buds and that i-cells become progressively restricted to specific regions within the zooids until they are mostly absent from the oldest zooids. The examined genes remain expressed in gametogenic regions. No evidence for i-cells is found in the stem between maturing zooids. Domains of high cell proliferation include regions where the examined genes are expressed, but also include some areas in which the examined genes were not expressed such as the stem within the growth zones. Cell proliferation in regions devoid of vasa-1, pl10, piwi, nanos-1, and nanos-2 expression indicates the presence of mitotically active epithelial cell lineages and, potentially, progenitor cell populations. CONCLUSIONS We provide the first evidence for i-cells in a siphonophore. Our findings suggest maintenance of i-cell populations at the sites of growth zones and that these sites are the main source of i-cells. This restriction of stem cells to particular regions in the colony, in combination with localized budding and spatial patterning during pro-bud subdivision, may play a major role in facilitating the precision of siphonophore growth. Spatially restricted maintenance of i-cells in mature zooids and absence of i-cells along the stem may explain the reduced developmental plasticity in older parts of the colony.
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Affiliation(s)
- Stefan Siebert
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St. Box GW, Providence, RI 02912 USA
| | - Freya E Goetz
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20004 Washington USA
| | - Samuel H Church
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St. Box GW, Providence, RI 02912 USA
| | - Pathikrit Bhattacharyya
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St. Box GW, Providence, RI 02912 USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St. Box GW, Providence, RI 02912 USA
| | | | - Casey W Dunn
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman St. Box GW, Providence, RI 02912 USA
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Abstract
In this review the history of discovery of siphonophores, from the first formal description by Carl Linnaeus in 1785 to the present, is summarized, and species richness together with a summary of world-wide distribution of this pelagic group within the clade Hydrozoa discussed. Siphonophores exhibit three basic body plans which are briefly explained and figured, whilst other atypical body plans are also noted. Currently, 175 valid siphonophore species are recognized in the latest WoRMS world list, including 16 families and 65 genera. Much new information since the last review in 1987 is revealed from the first molecular analysis of the group, enabling identification of some new morphological characters diagnostic for physonect siphonophores. Ten types of nematocysts (stinging cells) are identified in siphonophores, more than in any other cnidarian; these are incorporated into batteries in the side branches of the tentacles in most species (here termed tentilla), and tentilla are reviewed in the last section of this paper. Their discharge mechanisms are explained and also how the tentilla of several physonect siphonophores are modified into lures. Of particular interest is the recent discovery of a previously unknown red fluorescent lure in the tentilla of the deep sea physonect Erenna, the first described example of emission of red light by an invertebrate to attract prey.
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Affiliation(s)
- Gillian M. Mapstone
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- * E-mail:
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