1
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Lourtie A, Eeckhaut I, Mallefet J, Savarino P, Isorez M, Mussoi L, Bischoff H, Delroisse J, Hédouin L, Gerbaux P, Caulier G. Species-specific metabolites mediate host selection and larval recruitment of the symbiotic seastar shrimp. Sci Rep 2023; 13:12674. [PMID: 37542089 PMCID: PMC10403617 DOI: 10.1038/s41598-023-39527-2] [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: 05/12/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
In marine environments, host selection, defining how symbiotic organisms recognize and interact with their hosts, is often mediated by olfactory communication. Although adult symbionts may select their hosts detecting chemosensory cues, no information is available concerning the recruitment of symbiotic larvae which is a crucial step to sustain symbioses over generations. This study investigates the olfactory recognition of seastar hosts by adult Zenopontonia soror shrimps and the recruitment of their larvae. We examine the semiochemicals that influence host selection using chemical extractions, behavioural experiments in olfactometers, and mass spectrometry analyses. After describing the symbiotic population and the embryonic development of shrimps, our results demonstrate that asterosaponins, which are traditionally considered as chemical defences in seastars, are species-specific and play a role in attracting the symbiotic shrimps. Adult shrimps were found to be attracted only by their original host species Culcita novaeguineae, while larvae were attracted by different species of seastars. This study provides the first chemical identification of an olfactory cue used by larvae of symbiotic organisms to locate their host for recruitment. These findings highlight the importance of chemical communication in the mediation of symbiotic associations, which has broader significant implications for understanding the ecological dynamics of marine ecosystems.
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Affiliation(s)
- Alexia Lourtie
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium.
- Marine Biology Laboratory, Earth and Life Institute, University UCLouvain, Croix du sud 3/L7.06.04, 1348, Louvain-la-Neuve, Belgium.
| | - Igor Eeckhaut
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
- Belaza Marine Station (IH.SM-UMONS-ULIEGE), Toliara, Madagascar
| | - Jérôme Mallefet
- Marine Biology Laboratory, Earth and Life Institute, University UCLouvain, Croix du sud 3/L7.06.04, 1348, Louvain-la-Neuve, Belgium
| | - Philippe Savarino
- Organic Synthesis and Mass Spectrometry Laboratory, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Mathilde Isorez
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Lisa Mussoi
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Hugo Bischoff
- PSL Research University: EPHE-CNRS-UPVD, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Mo'orea, French Polynesia
- Laboratoire d'Excellence CORAIL, Mo'orea, French Polynesia
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Laetitia Hédouin
- PSL Research University: EPHE-CNRS-UPVD, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Mo'orea, French Polynesia
- Laboratoire d'Excellence CORAIL, Mo'orea, French Polynesia
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Guillaume Caulier
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons-UMONS, 23 Place du Parc, 7000, Mons, Belgium.
- Belaza Marine Station (IH.SM-UMONS-ULIEGE), Toliara, Madagascar.
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2
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Crinoid anthraquinones as kairomones allowing host selection for the symbiotic snapping shrimp Synalpheus stimpsonii. CHEMOECOLOGY 2022. [DOI: 10.1007/s00049-022-00368-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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3
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Dittami SM, Arboleda E, Auguet JC, Bigalke A, Briand E, Cárdenas P, Cardini U, Decelle J, Engelen AH, Eveillard D, Gachon CMM, Griffiths SM, Harder T, Kayal E, Kazamia E, Lallier FH, Medina M, Marzinelli EM, Morganti TM, Núñez Pons L, Prado S, Pintado J, Saha M, Selosse MA, Skillings D, Stock W, Sunagawa S, Toulza E, Vorobev A, Leblanc C, Not F. A community perspective on the concept of marine holobionts: current status, challenges, and future directions. PeerJ 2021; 9:e10911. [PMID: 33665032 PMCID: PMC7916533 DOI: 10.7717/peerj.10911] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/16/2021] [Indexed: 12/19/2022] Open
Abstract
Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
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Affiliation(s)
- Simon M Dittami
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Enrique Arboleda
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - Arite Bigalke
- Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Enora Briand
- Laboratoire Phycotoxines, Ifremer, Nantes, France
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ulisse Cardini
- Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Johan Decelle
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France
| | | | - Damien Eveillard
- Laboratoire des Sciences Numériques de Nantes (LS2N), Université de Nantes, CNRS, Nantes, France
| | - Claire M M Gachon
- Scottish Marine Institute, Scottish Association for Marine Science, Oban, United Kingdom
| | - Sarah M Griffiths
- School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | | | - Ehsan Kayal
- FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | | | - François H Lallier
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, University Park, United States of America
| | - Ezequiel M Marzinelli
- Ecology and Environment Research Centre, The University of Sydney, Sydney, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Sydney Institute of Marine Science, Mosman, Australia
| | | | - Laura Núñez Pons
- Section Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Soizic Prado
- Molecules of Communication and Adaptation of Microorganisms (UMR 7245), National Museum of Natural History, CNRS, Paris, France
| | - José Pintado
- Instituto de Investigaciones Marinas, CSIC, Vigo, Spain
| | - Mahasweta Saha
- Benthic Ecology, Helmholtz Center for Ocean Research, Kiel, Germany.,Marine Ecology and Biodiversity, Plymouth Marine Laboratory, Plymouth, United Kingdom
| | - Marc-André Selosse
- National Museum of Natural History, Département Systématique et Evolution, Paris, France.,Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Derek Skillings
- Philosophy Department, University of Pennsylvania, Philadelphia, United States of America
| | - Willem Stock
- Laboratory of Protistology & Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinichi Sunagawa
- Dept. of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH, Zürich, Switzerland
| | - Eve Toulza
- IHPE, Univ. de Montpellier, CNRS, IFREMER, UPDV, Perpignan, France
| | - Alexey Vorobev
- CEA - Institut de Biologie François Jacob, Genoscope, Evry, France
| | - Catherine Leblanc
- Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
| | - Fabrice Not
- Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France
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4
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Avino M, Ng GT, He Y, Renaud MS, Jones BR, Poon AFY. Tree shape-based approaches for the comparative study of cophylogeny. Ecol Evol 2019; 9:6756-6771. [PMID: 31312429 PMCID: PMC6618157 DOI: 10.1002/ece3.5185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 03/29/2019] [Indexed: 12/17/2022] Open
Abstract
Cophylogeny is the congruence of phylogenetic relationships between two different groups of organisms due to their long-term interaction. We investigated the use of tree shape distance measures to quantify the degree of cophylogeny. We implemented a reverse-time simulation model of pathogen phylogenies within a fixed host tree, given cospeciation probability, host switching, and pathogen speciation rates. We used this model to evaluate 18 distance measures between host and pathogen trees including two kernel distances that we developed for labeled and unlabeled trees, which use branch lengths and accommodate different size trees. Finally, we used these measures to revisit published cophylogenetic studies, where authors described the observed associations as representing a high or low degree of cophylogeny. Our simulations demonstrated that some measures are more informative than others with respect to specific coevolution parameters especially when these did not assume extreme values. For real datasets, trees' associations projection revealed clustering of high concordance studies suggesting that investigators are describing it in a consistent way. Our results support the hypothesis that measures can be useful for quantifying cophylogeny. This motivates their usage in the field of coevolution and supports the development of simulation-based methods, i.e., approximate Bayesian computation, to estimate the underlying coevolutionary parameters.
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Affiliation(s)
- Mariano Avino
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Garway T Ng
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Yiying He
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Mathias S Renaud
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada
| | - Bradley R Jones
- BC Centre for Excellence in HIV/AIDS Vancouver British Columbia Canada
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine Western University London Ontario Canada.,Department of Applied Mathematics Western University London Ontario Canada
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5
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Horká I, De Grave S, Fransen CHJM, Petrusek A, Ďuriš Z. Multiple host switching events shape the evolution of symbiotic palaemonid shrimps (Crustacea: Decapoda). Sci Rep 2016; 6:26486. [PMID: 27246395 PMCID: PMC4887867 DOI: 10.1038/srep26486] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 05/03/2016] [Indexed: 01/05/2023] Open
Abstract
The majority of the almost 1,000 species of Palaemonidae, the most speciose family of caridean shrimp, largely live in symbioses with marine invertebrates of different phyla. These associations range from weak epibiosis to obligatory endosymbiosis and from restricted commensalism to semi-parasitism, with the specialisation to particular hosts likely playing a role in the diversification of this shrimp group. Our study elucidates the evolutionary history of symbiotic palaemonids based on a phylogenetic analysis of 87 species belonging to 43 genera from the Indo-West Pacific and the Atlantic using two nuclear and two mitochondrial markers. A complementary three-marker analysis including taxa from GenBank raises this number to 107 species from 48 genera. Seven larger clades were recovered in the molecular phylogeny; the basal-most one includes mostly free-living shrimp, albeit with a few symbiotic species. Ancestral state reconstruction revealed that free-living forms likely colonised cnidarian hosts initially, and switching between different host phyla occurred multiple times in palaemonid evolutionary history. In some cases this was likely facilitated by the availability of analogous microhabitats in unrelated but morphologically similar host groups. Host switching and adaptations to newly colonised host groups must have played an important role in the evolution of this diverse shrimp group.
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Affiliation(s)
- Ivona Horká
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, and Institute of Environmental Technologies, Chittussiho 10, Ostrava, CZ-710 00, Czech Republic
- Charles University in Prague, Faculty of Science, Department of Ecology, Viničná 7, Prague, CZ-12844, Czech Republic
| | - Sammy De Grave
- Oxford University Museum of Natural History, Parks Road, Oxford, OX1 3PW, United Kingdom
| | - Charles H. J. M. Fransen
- Department of Marine Zoology, Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands
| | - Adam Petrusek
- Charles University in Prague, Faculty of Science, Department of Ecology, Viničná 7, Prague, CZ-12844, Czech Republic
| | - Zdeněk Ďuriš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, and Institute of Environmental Technologies, Chittussiho 10, Ostrava, CZ-710 00, Czech Republic
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6
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Herrera CS, Hirooka Y, Chaverri P. Pseudocospeciation of the mycoparasite Cosmospora with their fungal hosts. Ecol Evol 2016; 6:1504-14. [PMID: 27087926 PMCID: PMC4775519 DOI: 10.1002/ece3.1967] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 01/07/2023] Open
Abstract
Species of Cosmospora are parasites of other fungi (mycoparasites), including species belonging to the Xylariales. Based on prior taxonomic work, these fungi were determined to be highly host specific. We suspected that the association of Cosmospora and their hosts could not be a result of random chance, and tested the cospeciation of Cosmospora and the their hosts with contemporary methods (e.g., ParaFit, PACo, and Jane). The cophylogeny of Cosmospora and their hosts was found to be congruent, but only host‐parasite links in more recent evolutionary lineages of the host were determined as coevolutionary. Reconciliation reconstructions determined at least five host‐switch events early in the evolution of Cosmospora. Additionally, the rates of evolution between Cosmospora and their hosts were unequal. This pattern is more likely to be explained by pseudocospeciation (i.e., host switches followed by cospeciation), which also produces congruent cophylogenies.
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Affiliation(s)
- Cesar S Herrera
- Department of Plant Science and Landscape Architecture University of Maryland 2112 Plant Sciences Building College Park Maryland 20742 United States
| | - Yuuri Hirooka
- Department of Clinical Plant Science, Faculty of Bioscience Hosei University 3-7-2 Kajino-cho Koganei Tokyo Japan
| | - Priscila Chaverri
- Department of Plant Science and Landscape Architecture University of Maryland 2112 Plant Sciences Building College Park Maryland 20742 United States; Escuela de Biología Universidad de Costa Rica Apartado 11501-2060 San Pedro San José Costa Rica
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7
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Rouse GW, Lanterbecq D, Summers MM, Eeckhaut I. Four new species of Mesomyzostoma (Myzostomida: Annelida). J NAT HIST 2015. [DOI: 10.1080/00222933.2015.1056266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Greg W. Rouse
- Scripps Institution of Oceanography, UCSD, La Jolla, CA, USA
| | - Deborah Lanterbecq
- Laboratoire de Biologie des Organismes Marins et Biomimétisme, University of Mons, Mons, Belgium
- Laboratoire de Biotechnologie et Biologie Appliquée, Haute Ecole Provinciale de Hainaut-Condorcet, Ath, Belgium
| | | | - Igor Eeckhaut
- Laboratoire de Biologie des Organismes Marins et Biomimétisme, University of Mons, Mons, Belgium
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8
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Buckley HL, Rafat A, Ridden JD, Cruickshank RH, Ridgway HJ, Paterson AM. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity. PeerJ 2014; 2:e573. [PMID: 25250218 PMCID: PMC4168761 DOI: 10.7717/peerj.573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 08/20/2014] [Indexed: 11/20/2022] Open
Abstract
The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence and spatial genetic patterns and where greater sample replication was used, the amount of variation explained by partner genetic variation increased. Our results suggest that the phylogenetic congruence pattern, at least at small spatial scales, is likely due to reciprocal co-adaptation or co-dispersal. However, the detection of these patterns varies among different lichen taxa, across spatial scales and with different levels of sample replication. This work provides insight into the complexities faced in determining how evolutionary and ecological processes may interact to generate diversity in symbiotic association patterns at the population and community levels. Further, it highlights the critical importance of considering sample replication, taxonomic diversity and spatial scale in designing studies of co-diversification.
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Affiliation(s)
- Hannah L. Buckley
- Department of Ecology, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Arash Rafat
- Department of Ecology, Lincoln University, Lincoln, Canterbury, New Zealand
| | | | | | - Hayley J. Ridgway
- Department of Ecology, Lincoln University, Lincoln, Canterbury, New Zealand
| | - Adrian M. Paterson
- Department of Ecology, Lincoln University, Lincoln, Canterbury, New Zealand
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Summers MM, Rouse GW. Phylogeny of Myzostomida (Annelida) and their relationships with echinoderm hosts. BMC Evol Biol 2014; 14:170. [PMID: 25164680 PMCID: PMC4160548 DOI: 10.1186/s12862-014-0170-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 07/22/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adults (though starting life on the host inside cysts), while other taxa permanently reside in galls, cysts, or within the host's mouth, digestive system, coelom, or gonads. Myzostomid lifestyles range from stealing incoming food from the host's food grooves to consuming the host's tissue directly. Previous molecular studies of myzostomids have had limited sampling with respect to assessing the evolutionary relationships within the group; therefore molecular data from 75 myzostomid taxa were analyzed using maximum likelihood and maximum parsimony methods. To compare relationships of myzostomids with their hosts, a phylogeny was inferred for 53 hosts and a tanglegram constructed with 88 associations. RESULTS Gall- and some cyst-dwellers were recovered as a clade, while cyst-to-free-living forms were found as a grade including two clades of internal host-eaters (one infecting crinoids and the other asteroids and ophiuroids), mouth/digestive system inhabitants, and other cyst-dwellers. Clades of myzostomids were recovered that associated with asteroids, ophiuroids, and stalked or feather star crinoids. Co-phylogenetic analyses rejected a null-hypothesis of random associations at the global level, but not for individual associations. Event-based analyses relied most upon host-switching and duplication events to reconcile the association history. CONCLUSION Hypotheses were revised concerning the systematics and evolution of Myzostomida, as well their relationships to their hosts. We found two or three transitions between food-stealing and host-eating. Taxa that dwell within the mouth or digestive system and some cyst forms are arguably derived from cyst-to-free-living ancestors--possibly the result of a free-living form moving to the mouth and paedomorphic retention of the juvenile cyst. Phylogenetic conservatism in host use was observed among related myzostomid taxa. This finding suggests that myzostomids (which have a free-living planktonic stage) are limited to one or a few closely related hosts, despite most hosts co-occurring on the same reefs, many within physical contact of each other.
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Affiliation(s)
- Mindi M Summers
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA 92093 USA
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10
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Summers MM, Messing CG, Rouse GW. Phylogeny of Comatulidae (Echinodermata: Crinoidea: Comatulida): a new classification and an assessment of morphological characters for crinoid taxonomy. Mol Phylogenet Evol 2014; 80:319-39. [PMID: 25065346 DOI: 10.1016/j.ympev.2014.06.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/15/2014] [Accepted: 06/21/2014] [Indexed: 11/29/2022]
Abstract
Comatulidae Fleming, 1828 (previously, and incorrectly, Comasteridae A.H. Clark, 1908a), is a group of feather star crinoids currently divided into four accepted subfamilies, 21 genera and approximately 95 nominal species. Comatulidae is the most commonly-encountered and species-rich crinoid group on shallow tropical coral reefs, particularly in the Indo-western Pacific region (IWP). We conducted a molecular phylogenetic analysis of the group with concatenated data from up to seven genes for 43 nominal species spanning 17 genera and all subfamilies. Basal nodes returned low support, but maximum likelihood, maximum parsimony, and Bayesian analyses were largely congruent, permitting an evaluation of current taxonomy and analysis of morphological character transformations. Two of the four current subfamilies were paraphyletic, whereas 15 of the 17 included genera returned as monophyletic. We provide a new classification with two subfamilies, Comatulinae and Comatellinae n. subfamily Summers, Messing, & Rouse, the former containing five tribes. We revised membership of analyzed genera to make them all clades and erected Anneissia n. gen. Summers, Messing, & Rouse. Transformation analyses for morphological features generally used in feather star classification (e.g., ray branching patterns, articulations) and those specifically for Comatulidae (e.g., comb pinnule form, mouth placement) were labile with considerable homoplasy. These traditional characters, in combination, allow for generic diagnoses, but in most cases we did not recover apomorphies for subfamilies, tribes, and genera. New morphological characters that will be informative for crinoid taxonomy and identification are still needed. DNA sequence data currently provides the most reliable method of identification to the species-level for many taxa of Comatulidae.
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Affiliation(s)
- Mindi M Summers
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Charles G Messing
- Oceanographic Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL 33004, USA
| | - Greg W Rouse
- Scripps Institution of Oceanography, UCSD, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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11
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Boyko CB, Moss J, Williams JD, Shields JD. A molecular phylogeny of Bopyroidea and Cryptoniscoidea (Crustacea: Isopoda). SYST BIODIVERS 2013. [DOI: 10.1080/14772000.2013.865679] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Phylogenetic evidence for recent diversification of obligate coral-dwelling gobies compared with their host corals. Mol Phylogenet Evol 2013; 69:123-32. [PMID: 23680856 PMCID: PMC4047829 DOI: 10.1016/j.ympev.2013.04.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Revised: 04/24/2013] [Accepted: 04/29/2013] [Indexed: 11/23/2022]
Abstract
The coral reef-dwelling genus Gobiodon diversified within the last 10 My. Acroporid hosts of Gobiodon fishes have radiated since the Eocene (49 Mya). Despite a mutualistic association Gobiodon fishes did not co-speciate with corals. Testing dates of diversification is fundamental before assuming co-speciation. Phylogenetics of Gobiodon differ in part with previous morphological analyses.
The rich diversity of coral reef organisms is supported, at least in part, by the diversity of coral reef habitat. Some of the most habitat specialised fishes on coral reefs are obligate coral-dwelling gobies of the genus Gobiodon that inhabit a range of coral species, mostly of the genus Acropora. However, the role of this specialised pattern of habitat use in the evolution of coral-dwelling gobies is not well understood. Diversification of coral-dwelling gobies may be driven by the diversification of their host corals (cospeciation), or alternatively, diversification of these fishes may have occurred independently of the diversification of host corals. The cospeciation hypothesis assumes similar timing in evolution of the gobies and their host corals. We used four genes for each group and the available fossil records to reconstruct and date phylogenies for 20 species of Gobiodon from the Indo-Pacific and the Red Sea, and for 28 species of the coral genus Acropora. Our results indicate that Gobiodon diversified mostly in the last ∼5 My, whereas Acropora corals have consistently diversified since the Eocene, making the hypothesis of cospeciation untenable. The fully resolved molecular phylogeny of the genus Gobiodon is in part at odds with previous analyses incorporating morphological data and indicates that some morphological traits form paraphyletic clades within Gobiodon. Our phylogeny supports a hypothesis in which Gobiodon diversified in the Indo-Pacific Ocean and then radiated recently, with multiple new variants found in the Red Sea.
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de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. THE NEW PHYTOLOGIST 2013; 198:347-385. [PMID: 23437795 DOI: 10.1111/nph.12150] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/19/2012] [Indexed: 05/26/2023]
Abstract
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host-symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host-parasite and host-mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host-symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.
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Affiliation(s)
- D M de Vienne
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - G Refrégier
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91405, Orsay, France
- CNRS, UMR8621, 91405, Orsay, France
| | - M López-Villavicencio
- Muséum National d'Histoire Naturelle, 57 rue Cuvier, F-75231, Paris Cedex 05, France
| | - A Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85354, Freising, Germany
| | - M E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - T Giraud
- Université Paris-Sud, Ecologie, Systématique et Evolution, UMR 8079, 91405, Orsay, France
- CNRS, UMR8079, 91405, Orsay, France
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McFrederick QS, Taylor DR. Evolutionary history of nematodes associated with sweat bees. Mol Phylogenet Evol 2012; 66:847-56. [PMID: 23159895 DOI: 10.1016/j.ympev.2012.11.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 11/30/2022]
Abstract
Organisms that live in close association with other organisms make up a large part of the world's diversity. One driver of this diversity is the evolution of host-species specificity, which can occur via reproductive isolation following a host-switch or, given the correct circumstances, via cospeciation. In this study, we explored the diversity and evolutionary history of Acrostichus nematodes that are associated with halictid bees in North America. First, we conducted surveys of bees in Virginia, and found six halictid species that host Acrostichus. To test the hypothesis of cospeciation, we constructed phylogenetic hypotheses of Acrostichus based on three genes. We found Acrostichus puri and Acrostichus halicti to be species complexes comprising cryptic, host-specific species. Although several nodes in the host and symbiont phylogenies were congruent and tests for cospeciation were significant, the host's biogeography, the apparent patchiness of the association across the host's phylogeny, and the amount of evolution in the nematode sequence suggested a mixture of cospeciation, host switching, and extinction events instead of strict cospeciation. Cospeciation can explain the relationships between Ac. puri and its augochlorine hosts, but colonization of Halictus hosts is more likely than cospeciation. The nematodes are vertically transmitted, but sexual transmission is also likely. Both of these transmission modes may explain host-species specificity and congruent bee and nematode phylogenies. Additionally, all halictid hosts come from eusocial or socially polymorphic lineages, suggesting that sociality may be a factor in the suitability of hosts for Acrostichus.
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Affiliation(s)
- Quinn S McFrederick
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, United States.
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Fixed, free, and fixed: the fickle phylogeny of extant Crinoidea (Echinodermata) and their Permian-Triassic origin. Mol Phylogenet Evol 2012; 66:161-81. [PMID: 23063883 DOI: 10.1016/j.ympev.2012.09.018] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 08/13/2012] [Accepted: 09/17/2012] [Indexed: 11/21/2022]
Abstract
Although the status of Crinoidea (sea lilies and featherstars) as sister group to all other living echinoderms is well-established, relationships among crinoids, particularly extant forms, are debated. All living species are currently placed in Articulata, which is generally accepted as the only crinoid group to survive the Permian-Triassic extinction event. Recent classifications have recognized five major extant taxa: Isocrinida, Hyocrinida, Bourgueticrinina, Comatulidina and Cyrtocrinida, plus several smaller groups with uncertain taxonomic status, e.g., Guillecrinus, Proisocrinus and Caledonicrinus. Here we infer the phylogeny of extant Crinoidea using three mitochondrial genes and two nuclear genes from 59 crinoid terminals that span the majority of extant crinoid diversity. Although there is poor support for some of the more basal nodes, and some tree topologies varied with the data used and mode of analysis, we obtain several robust results. Cyrtocrinida, Hyocrinida, Isocrinida are all recovered as clades, but two stalked crinoid groups, Bourgueticrinina and Guillecrinina, nest among the featherstars, lending support to an argument that they are paedomorphic forms. Hence, they are reduced to families within Comatulida. Proisocrinus is clearly shown to be part of Isocrinida, and Caledonicrinus may not be a bourgueticrinid. Among comatulids, tree topologies show little congruence with current taxonomy, indicating that much systematic revision is required. Relaxed molecular clock analyses with eight fossil calibration points recover Articulata with a median date to the most recent common ancestor at 231-252mya in the Middle to Upper Triassic. These analyses tend to support the hypothesis that the group is a radiation from a small clade that passed through the Permian-Triassic extinction event rather than several lineages that survived. Our tree topologies show various scenarios for the evolution of stalks and cirri in Articulata, so it is clear that further data and taxon sampling are needed to recover a more robust phylogeny of the group.
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The evolutionary ecology of biotic association in a megadiverse bivalve superfamily: sponsorship required for permanent residency in sediment. PLoS One 2012; 7:e42121. [PMID: 22905116 PMCID: PMC3414514 DOI: 10.1371/journal.pone.0042121] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Marine lineage diversification is shaped by the interaction of biotic and abiotic factors but our understanding of their relative roles is underdeveloped. The megadiverse bivalve superfamily Galeommatoidea represents a promising study system to address this issue. It is composed of small-bodied clams that are either free-living or have commensal associations with invertebrate hosts. To test if the evolution of this lifestyle dichotomy is correlated with specific ecologies, we have performed a statistical analysis on the lifestyle and habitat preference of 121 species based on 90 source documents. METHODOLOGY/PRINCIPAL FINDINGS Galeommatoidea has significant diversity in the two primary benthic habitats: hard- and soft-bottoms. Hard-bottom dwellers are overwhelmingly free-living, typically hidden within crevices of rocks/coral heads/encrusting epifauna. In contrast, species in soft-bottom habitats are almost exclusively infaunal commensals. These infaunal biotic associations may involve direct attachment to a host, or clustering around its tube/burrow, but all commensals locate within the oxygenated sediment envelope produced by the host's bioturbation. CONCLUSIONS/SIGNIFICANCE the formation of commensal associations by Galeommatoidean clams is robustly correlated with an abiotic environmental setting: living in sediments (P < 0.001). Sediment-dwelling bivalves are exposed to intense predation pressure that drops markedly with depth of burial. Commensal galeommatoideans routinely attain depth refuges many times their body lengths, independent of siphonal investment, by virtue of their host's burrowing and bioturbation. In effect, they use their much larger hosts as giant auto-irrigating siphon substitutes. The evolution of biotic associations with infaunal bioturbating hosts may have been a prerequisite for the diversification of Galeommatoidea in sediments and has likely been a key factor in the success of this exceptionally diverse bivalve superfamily.
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Hartmann S, Helm C, Nickel B, Meyer M, Struck TH, Tiedemann R, Selbig J, Bleidorn C. Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS One 2012; 7:e29843. [PMID: 22276131 PMCID: PMC3262807 DOI: 10.1371/journal.pone.0029843] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 12/06/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms. METHODOLOGY Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. CONCLUSIONS Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.
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Affiliation(s)
- Stefanie Hartmann
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Conrad Helm
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
| | - Birgit Nickel
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Leipzig, Germany
| | | | - Ralph Tiedemann
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Joachim Selbig
- Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Bleidorn
- University of Leipzig, Institute for Biology II, Molecular Evolution and Systematics of Animals, Leipzig, Germany
- Department of Evolutionary Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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