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Anthony CJ, Bentlage B, Helm RR. Animal evolution at the ocean's water-air interface. Curr Biol 2024; 34:196-203.e2. [PMID: 38194916 DOI: 10.1016/j.cub.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/28/2023] [Accepted: 11/07/2023] [Indexed: 01/11/2024]
Abstract
Innovation is a key to evolutionary success and entrance into novel ecosystems.1 Species that float freely at the ocean's surface, termed obligate neuston (also called pleuston, here referred to simply as neuston), include highly specialized taxa from distinct evolutionary lineages that evolved floating morphologies.2 In 1958, Soviet scientist, A.I. Savilov,3 stated that floating animal species are derived from benthic ancestors, rather than species from the adjacent pelagic zone, and that floating morphologies are homologous to benthic attachment structures. To test Savilov's hypothesis, we constructed molecular phylogenies and ancestral states for all major floating groups for which molecular data were available. Our results reveal that four of the five clades examined arose directly from a substrate-attached ancestor, although that substrate was not necessarily the benthos, as Savilov stated, and instead included epibiotic and rafting ancestors. Despite their diverse evolutionary origins, floating animals use gas-trapping mechanisms to remain at the surface,4,5,6 and many of these gas-trapping structures appear to be homologous to substrate attachment structures. We also reconstruct the trophic habits of floating mollusks and their sister species, revealing that prey preference remains conserved upon entering the ocean's surface ecosystem. Colonization of the ocean's surface seems to have occurred through successive evolutionary steps from the seafloor. Our results suggest that these steps often included transitions through epibiotic (where species attach to other living organisms) or rafting (where species attach to floating debris) habits. The water-air interface, despite its unique properties, may, in some ways, be just another substrate.
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Affiliation(s)
- Colin J Anthony
- Marine Laboratory, University of Guam, Mangilao, Guam 96913, USA
| | - Bastian Bentlage
- Marine Laboratory, University of Guam, Mangilao, Guam 96913, USA
| | - Rebecca R Helm
- Earth Commons Institute, Georgetown University, Washington, DC 20057, USA.
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2
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Tessnow-von Wysocki I, Wang M, Morales-Caselles C, Woodall LC, Syberg K, Carney Almroth B, Fernandez M, Monclús L, Wilson SP, Warren M, Knoblauch D, Helm RR. Plastics treaty text must center ecosystems. Science 2023; 382:525-526. [PMID: 37917703 DOI: 10.1126/science.adl3202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Affiliation(s)
| | - Mengjiao Wang
- Greenpeace Research Laboratories, Department of Bioscience, University of Exeter, Exeter, UK
| | - Carmen Morales-Caselles
- Department of Biology, University of Cadiz, Instituto Universitario de Investigación Marina, Puerto Real, Cádiz, Spain
| | - Lucy C Woodall
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
- Deep Ocean Stewardship Initiative, University of Southampton, Southampton, UK
| | - Kristian Syberg
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Bethanie Carney Almroth
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marina Fernandez
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Laura Monclús
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | | | - Rebecca R Helm
- Georgetown University Earth Commons Institute, Washington, DC, USA
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3
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Chong F, Spencer M, Maximenko N, Hafner J, McWhirter AC, Helm RR. High concentrations of floating neustonic life in the plastic-rich North Pacific Garbage Patch. PLoS Biol 2023; 21:e3001646. [PMID: 37141195 PMCID: PMC10159152 DOI: 10.1371/journal.pbio.3001646] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/23/2023] [Indexed: 05/05/2023] Open
Abstract
Floating life (obligate neuston) is a core component of the ocean surface food web. However, only 1 region of high neustonic abundance is known so far, the Sargasso Sea in the Subtropical North Atlantic gyre, where floating life provides critical habitat structure and ecosystem services. Here, we hypothesize that floating life is also concentrated in other gyres with converging surface currents. To test this hypothesis, we collected samples through the eastern North Pacific Subtropical Gyre in the area of the North Pacific "Garbage Patch" (NPGP) known to accumulate floating anthropogenic debris. We found that densities of floating life were higher inside the central NPGP than on its periphery and that there was a positive relationship between neuston abundance and plastic abundance for 3 out of 5 neuston taxa, Velella, Porpita, and Janthina. This work has implications for the ecology of subtropical oceanic gyre ecosystems.
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Affiliation(s)
- Fiona Chong
- Energy and Environment Institute, University of Hull, Hull, United Kingdom
- School of Environmental Sciences, University of Hull, Hull, United Kingdom
| | - Matthew Spencer
- School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nikolai Maximenko
- International Pacific Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Jan Hafner
- International Pacific Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Andrew C McWhirter
- Center for Marine Debris Research, Hawai'i Pacific University, Waimanalo, Hawaii, United States of America
| | - Rebecca R Helm
- The Earth Commons, Georgetown University, Washington, DC, United States of America
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4
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Helm RR, Clark N, Harden-Davies H, Amon D, Girguis P, Bordehore C, Earle S, Gibbons MJ, Golbuu Y, Haddock SHD, Houghton JDR, Javidpour J, McCauley DJ, Morgan L, Obura D, Pakhomov EA, Pitt KA, Ramon JJ, Sumaila R, Thiebot JB. Protect high seas biodiversity. Science 2021; 372:1048-1049. [PMID: 34083479 DOI: 10.1126/science.abj0581] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Rebecca R Helm
- University of North Carolina Asheville, Asheville, NC 28804, USA. .,Smithsonian Institution National Museum of Natural History, Washington, DC 20560, USA
| | - Nichola Clark
- Australian National Centre for Ocean Resources and Security, University of Wollongong, Wollongong NSW 2522, Australia.,The Pew Charitable Trusts, Washington, DC 20004, USA
| | - Harriet Harden-Davies
- Australian National Centre for Ocean Resources and Security, University of Wollongong, Wollongong NSW 2522, Australia.,Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Diva Amon
- SpeSeas, D'Abadie, Trinidad and Tobago.,Natural History Museum, London, UK
| | - Peter Girguis
- Harvard University, Cambridge, MA 02138, USA.,Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Cesar Bordehore
- Multidisciplinary Institute for Environmental Studies "Ramon Margalef" and Department of Ecology, University of Alicante, 03690 Alicante, Spain
| | | | - Mark J Gibbons
- University of the Western Cape, Bellville 7535, Republic of South Africa
| | | | | | - Jonathan D R Houghton
- School of Biological Sciences, Queen's University Belfast, BT9 7DL, Northern Ireland
| | - Jamileh Javidpour
- Department of Biology, University of Southern Denmark, 5230 Odense-M, Denmark
| | - Douglas J McCauley
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Lance Morgan
- Marine Conservation Institute, Seattle, WA 98103, USA
| | | | - Evgeny A Pakhomov
- Earth, Ocean and Atmospheric Sciences Department and the Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Kylie A Pitt
- School of Environment and Science, Griffith University, Southport, QLD 4222, Australia
| | | | - Rashid Sumaila
- University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Tarrant AM, Helm RR, Levy O, Rivera HE. Environmental entrainment demonstrates natural circadian rhythmicity in the cnidarian Nematostella vectensis. ACTA ACUST UNITED AC 2019; 222:jeb.205393. [PMID: 31611292 DOI: 10.1242/jeb.205393] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
Considerable advances in chronobiology have been made through controlled laboratory studies, but distinct temporal rhythms can emerge under natural environmental conditions. Lab-reared Nematostella vectensis sea anemones exhibit circadian behavioral and physiological rhythms. Given that these anemones inhabit shallow estuarine environments subject to tidal inputs, it was unclear whether circadian rhythmicity would persist following entrainment in natural conditions, or whether circatidal periodicity would predominate. Nematostella were conditioned within a marsh environment, where they experienced strong daily temperature cycles as well as brief tidal flooding around the full and new moons. Upon retrieval, anemones exhibited strong circadian (∼24 h) activity rhythms under a light-dark cycle or continuous darkness, but reduced circadian rhythmicity under continuous light. However, some individuals in each light condition showed circadian rhythmicity, and a few individuals showed circatidal rhythmicity. Consistent with the behavioral studies, a large number of transcripts (1640) exhibited diurnal rhythmicity compared with very few (64) with semidiurnal rhythmicity. Diurnal transcripts included core circadian regulators, and 101 of 434 (23%) genes that were previously found to be upregulated by exposure to ultraviolet radiation. Together, these behavioral and transcriptional studies show that circadian rhythmicity predominates and suggest that solar radiation drives physiological cycles in this sediment-dwelling subtidal animal.
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Affiliation(s)
- Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA 02543, USA
| | - Rebecca R Helm
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA 02543, USA.,Biology Department, University of North Carolina Asheville, Asheville NC 28804, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Hanny E Rivera
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole MA 02543, USA.,Biology Department, Boston University, Boston MA 02215, USA
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Helm RR. Evolution and development of scyphozoan jellyfish. Biol Rev Camb Philos Soc 2018; 93:1228-1250. [DOI: 10.1111/brv.12393] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Rebecca R. Helm
- Woods Hole Oceanographic Institution – Biology, Mailstop 33, 45 Water Street Woods Hole MA 01543 U.S.A
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Abstract
Many animals go through one or more metamorphoses during their lives, however, the molecular underpinnings of metamorphosis across diverse species are not well understood. Medusozoa (Cnidaria) is a clade of animals with complex life cycles, these life cycles can include a polyp stage that metamorphoses into a medusa (jellyfish). Medusae are produced through a variety of different developmental mechanisms-in some species polyps bud medusae (Hydrozoa), in others medusae are formed through polyp fission (Scyphozoa), while in others medusae are formed through direct transformation of the polyp (Cubozoa). To better understand the molecular mechanisms that may coordinate these different forms of metamorphosis, we tested two compounds first identified to induce metamorphosis in the moon jellyfish Aurelia aurita (indomethacin and 5-methoxy-2-methylindole) on a broad diversity of medusozoan polyps. We discovered that indole-containing compounds trigger metamorphosis across a broad diversity of species. All tested discomedusan polyps metamorphosed in the presence of both compounds, including species representatives of several major lineages within the clade (Pelagiidae, Cyaneidae, both clades of Rhizostomeae). In a cubozoan, low levels of 5-methoxy-2-methylindole reliably induced complete and healthy metamorphosis. In contrast, neither compound induced medusa metamorphosis in a coronate scyphozoan, or medusa production in either hydrozoan tested. Our results support the hypothesis that metamorphosis is mediated by a conserved induction pathway within discomedusan scyphozoans, and possibly cubozoans. However, failure of these compounds to induce metamorphosis in a coronate suggests this induction mechanism may have been lost in this clade, or is convergent between Scyphozoa and Cubozoa.
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Affiliation(s)
- Rebecca R. Helm
- Brown University, Providence, RI, United States of America
- Woods Hole Oceanographic Institution, Woods Hole, MA, United States of America
- * E-mail:
| | - Casey W. Dunn
- Brown University, Providence, RI, United States of America
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Ricci L, Chaurasia A, Lapébie P, Dru P, Helm RR, Copley RR, Tiozzo S. Identification of differentially expressed genes from multipotent epithelia at the onset of an asexual development. Sci Rep 2016; 6:27357. [PMID: 27264734 PMCID: PMC4893630 DOI: 10.1038/srep27357] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/17/2016] [Indexed: 11/19/2022] Open
Abstract
Organisms that have evolved alternative modes of reproduction, complementary to the sexual mode, are found across metazoans. The chordate Botryllus schlosseri is an emerging model for asexual development studies. Botryllus can rebuild its entire body from a portion of adult epithelia in a continuous and stereotyped process called blastogenesis. Anatomy and ontogenies of blastogenesis are well described, however molecular signatures triggering this developmental process are entirely unknown. We isolated tissues at the site of blastogenesis onset and from the same epithelia where this process is never triggered. We linearly amplified an ultra-low amount of mRNA (<10ng) and generated three transcriptome datasets. To provide a conservative landscape of transcripts differentially expressed between blastogenic vs. non-blastogenic epithelia we compared three different mapping and analysis strategies with a de novo assembled transcriptome and partially assembled genome as references, additionally a self-mapping strategy on the dataset. A subset of differentially expressed genes were analyzed and validated by in situ hybridization. The comparison of different analyses allowed us to isolate stringent sets of target genes, including transcripts with potential involvement in the onset of a non-embryonic developmental pathway. The results provide a good entry point to approach regenerative event in a basal chordate.
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Affiliation(s)
- Lorenzo Ricci
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Ankita Chaurasia
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Pascal Lapébie
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Philippe Dru
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Rebecca R Helm
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Richard R Copley
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
| | - Stefano Tiozzo
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, 06230, Villefranche-sur-mer, France
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9
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Helm RR, Tiozzo S, Lilley MKS, Lombard F, Dunn CW. Comparative muscle development of scyphozoan jellyfish with simple and complex life cycles. EvoDevo 2015; 6:11. [PMID: 25932322 PMCID: PMC4415277 DOI: 10.1186/s13227-015-0005-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Simple life cycles arise from complex life cycles when one or more developmental stages are lost. This raises a fundamental question - how can an intermediate stage, such as a larva, be removed, and development still produce a normal adult? To address this question, we examined the development in several species of pelagiid jellyfish. Most members of Pelagiidae have a complex life cycle with a sessile polyp that gives rise to ephyrae (juvenile medusae); but one species within Pelagiidae, Pelagia noctiluca, spends its whole life in the water column, developing from a larva directly into an ephyra. In many complex life cycles, adult features develop from cell populations that remain quiescent in larvae, and this is known as life cycle compartmentalization and may facilitate the evolution of direct life cycles. A second type of metamorphic processes, known as remodeling, occurs when adult features are formed through modification of already differentiated larval structures. We examined muscle morphology to determine which of these alternatives may be present in Pelagiidae. Results We first examined the structure and development of polyp and ephyra musculature in Chrysaora quinquecirrha, a close relative of P. noctiluca with a complex life cycle. Using phallotoxin staining and confocal microscopy, we verified that polyps have four to six cord muscles that persist in strobilae and discovered that cord muscles is physically separated from ephyra muscle. When cord muscle is removed from ephyra segments, normal ephyra muscle still develops. This suggests that polyp cord muscle is not necessary for ephyra muscle formation. We also found no evidence of polyp-like muscle in P. noctiluca. In both species, we discovered that ephyra muscle arises de novo in a similar manner, regardless of the life cycle. Conclusions The separate origins of polyp and ephyra muscle in C. quinquecirrha and the absence of polyp-like muscle in P. noctiluca suggest that polyp muscle is not remodeled to form ephyra muscle in Pelagiidae. Life cycle stages in Scyphozoa may instead be compartmentalized. Because polyp muscle is not directly remodeled, this may have facilitated the loss of the polyp stage in the evolution of P. noctiluca. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0005-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rebecca R Helm
- Brown University, 80 Waterman St. Box GW, Providence, 02912 RI USA
| | - Stefano Tiozzo
- CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Sorbonne Universités, UPMC Univ Paris 06, Observatoire Océanographique, 06230 Villefranche-sur-mer, France
| | - Martin K S Lilley
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7093, LOV, Observatoire Océanologique, 06230 Villefranche-sur-mer, France ; Current address: School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS UK
| | - Fabien Lombard
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7093, LOV, Observatoire Océanologique, 06230 Villefranche-sur-mer, France
| | - Casey W Dunn
- Brown University, 80 Waterman St. Box GW, Providence, 02912 RI USA
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McClain CR, Balk MA, Benfield MC, Branch TA, Chen C, Cosgrove J, Dove ADM, Gaskins L, Helm RR, Hochberg FG, Lee FB, Marshall A, McMurray SE, Schanche C, Stone SN, Thaler AD. Sizing ocean giants: patterns of intraspecific size variation in marine megafauna. PeerJ 2015; 3:e715. [PMID: 25649000 PMCID: PMC4304853 DOI: 10.7717/peerj.715] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/10/2014] [Indexed: 11/20/2022] Open
Abstract
What are the greatest sizes that the largest marine megafauna obtain? This is a simple question with a difficult and complex answer. Many of the largest-sized species occur in the world’s oceans. For many of these, rarity, remoteness, and quite simply the logistics of measuring these giants has made obtaining accurate size measurements difficult. Inaccurate reports of maximum sizes run rampant through the scientific literature and popular media. Moreover, how intraspecific variation in the body sizes of these animals relates to sex, population structure, the environment, and interactions with humans remains underappreciated. Here, we review and analyze body size for 25 ocean giants ranging across the animal kingdom. For each taxon we document body size for the largest known marine species of several clades. We also analyze intraspecific variation and identify the largest known individuals for each species. Where data allows, we analyze spatial and temporal intraspecific size variation. We also provide allometric scaling equations between different size measurements as resources to other researchers. In some cases, the lack of data prevents us from fully examining these topics and instead we specifically highlight these deficiencies and the barriers that exist for data collection. Overall, we found considerable variability in intraspecific size distributions from strongly left- to strongly right-skewed. We provide several allometric equations that allow for estimation of total lengths and weights from more easily obtained measurements. In several cases, we also quantify considerable geographic variation and decreases in size likely attributed to humans.
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Affiliation(s)
- Craig R McClain
- National Evolutionary Synthesis Center , Durham, NC , USA ; Department of Biology, Duke University , Durham, NC , USA
| | - Meghan A Balk
- Department of Biology, University of New Mexico , Albuquerque, NM , USA
| | - Mark C Benfield
- Department of Oceanography and Coastal Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Trevor A Branch
- School of Aquatic & Fishery Sciences, University of Washington , Seattle, WA , USA
| | - Catherine Chen
- Department of Biology, Duke University , Durham, NC , USA
| | - James Cosgrove
- Natural History Section, Royal British Columbia Museum , Victoria, BC , Canada
| | | | - Leo Gaskins
- Department of Biology, Duke University , Durham, NC , USA
| | - Rebecca R Helm
- Department of Ecology and Evolutionary Biology, Brown University , Providence, RI , USA
| | - Frederick G Hochberg
- Department of Invertebrate Zoology, Santa Barbara Museum of Natural History , Santa Barbara, CA , USA
| | - Frank B Lee
- Department of Biology, Duke University , Durham, NC , USA
| | | | - Steven E McMurray
- Department of Biology and Marine Biology, University of North Carolina Wilmington , Wilmington, NC , USA
| | | | - Shane N Stone
- Department of Biology, Duke University , Durham, NC , USA
| | - Andrew D Thaler
- Blackbeard Biologic: Science and Environmental Advisors , Vallejo, CA , USA
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11
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Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SHD, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PLoS One 2011; 6:e22953. [PMID: 21829563 PMCID: PMC3146525 DOI: 10.1371/journal.pone.0022953] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 07/01/2011] [Indexed: 02/02/2023] Open
Abstract
We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing.
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Affiliation(s)
- Stefan Siebert
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SS); (CWD)
| | - Mark D. Robinson
- Epigenetics Laboratory, Cancer Research Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sophia C. Tintori
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Freya Goetz
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Rebecca R. Helm
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
| | - Stephen A. Smith
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Nathan Shaner
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America
| | - Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SS); (CWD)
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