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Pankey MS, Gochfeld DJ, Gastaldi M, Macartney KJ, Clayshulte Abraham A, Slattery M, Lesser MP. Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin. Mol Ecol 2024; 33:e17321. [PMID: 38529721 DOI: 10.1111/mec.17321] [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: 05/31/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024]
Abstract
Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.
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Affiliation(s)
- M S Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - D J Gochfeld
- National Center for Natural Products Research and Environmental Toxicology, University of Mississippi, University, Mississippi, USA
| | - M Gastaldi
- Escuela Superior de Ciencias Marinas-Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
| | - K J Macartney
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - A Clayshulte Abraham
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M Slattery
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M P Lesser
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Ngwakum BB, Payne RP, Teske PR, Janson L, Kerwath SE, Samaai T. Hundreds of new DNA barcodes for South African sponges. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1915896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Benedicta B. Ngwakum
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Robyn P. Payne
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Liesl Janson
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
| | - Sven E. Kerwath
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
- Department of Forestry, Fisheries and the Environment, Fisheries Branch, Fisheries Research, Private Bag X2, Roggebaai, Cape Town, 8012, Western Cape, South Africa
| | - Toufiek Samaai
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, Cape Town, South Africa
- Department of Forestry, Fisheries and the Environment, Oceans & Coasts Branch, Oceans & Coasts Research, Private Bag X4390, Cape Town, 8001, Western Cape, South Africa
- Department of Biological Sciences, University of Cape Town, Private Bag X 3, Rondebosch, Cape Town, 7701, South Africa
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3
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Rindi F, Pasella MM, Lee MFE, Verbruggen H. Phylogeography of the mediterranean green seaweed Halimeda tuna (Ulvophyceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2020; 56:1109-1113. [PMID: 32315445 DOI: 10.1111/jpy.13006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Populations of many Mediterranean marine species show a strong phylogeographic structure, but the knowledge available for native seaweeds is limited. We investigated the genetic diversity of the green alga Halimeda tuna based on two plastid markers (tufA gene and a newly developed amplicon spanning five ribosomal protein genes and intergenic spacers, the rpl2-rpl14 region). The tufA sequences showed that Mediterranean H. tuna represents a single, well-defined species. The rpl2-rpl14 results highlighted a genetic separation between western and eastern Mediterranean populations; specimens collected from widely scattered locations in the Adriatic/Ionian region shared a haplotype unique to this region, and formed a group separated from all western Mediterranean regions. Specimens from Sardinia also formed a unique haplotype. Within the western Mediterranean basin, a gradual shift in the frequency of haplotypes was apparent along a West-East gradient. Our results represent the first clear evidence of an East-West genetic cleavage in a native Mediterranean macroalga and offer an interesting perspective for further research into fine-scale seaweed population structure in the NW Mediterranean Sea.
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Affiliation(s)
- Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, Ancona, 60131, Italy
| | - Marisa M Pasella
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
| | - Ming-Fen E Lee
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
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PAcheco C, Carballo JL, Cruz-Barraza JA, Schönberg CHL, Calcinai B. Delimiting boundaries between species: excavating sponges close to Cliona mucronata (Demospongiae). SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1776785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Cristian PAcheco
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, México
| | - José Luis Carballo
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, México
| | - JosÉ Antonio Cruz-Barraza
- Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, México
| | - Christine Hanna Lydia Schönberg
- Oceans Graduate School and UWA Oceans Institute, the University of Western Australia, Crawley, Western Australia
- Aquatic Zoology, Western Australian Museum, Welshpool, Western Australia
| | - Barbara Calcinai
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Le Marche, Italia
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Erpenbeck D, Steiner M, Schuster A, Genner MJ, Manconi R, Pronzato R, Ruthensteiner B, van den Spiegel D, van Soest RWM, Wörheide G. Minimalist barcodes for sponges: a case study classifying African freshwater Spongillida. Genome 2018; 62:1-10. [PMID: 30557098 DOI: 10.1139/gen-2018-0098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
African sponges, particularly freshwater sponges, are understudied relative to demosponges in most other geographical regions. Freshwater sponges (Spongillida) likely share a common ancestor; however, their evolutionary history, particularly during their radiation into endemic and allegedly cosmopolitan groups, is unclear. Freshwater sponges of at least 58 species of 17 genera and four families are described from Central and Eastern Africa, but the diversity is underestimated due to limited distinguishable morphological features. The discovery of additional cryptic species is very likely with the use of molecular techniques such as DNA barcoding. The Royal Museum of Central Africa (MRAC, Tervuren, Belgium) hosts one of the largest collections of (Central) African freshwater sponge type material. Type specimens in theory constitute ideal targets for molecular taxonomy; however, the success is frequently hampered by DNA degradation and deamination, which are a consequence of suboptimal preservation techniques. Therefore, we genotyped African demosponge holotype material of the MRAC with specific short primers suitable for degenerated tissue and compare the results with the current, morphology-based classification. Our results demonstrate the utility of minimalistic barcodes for identification of sponges, potentially enabling efficient identification of individuals in taxonomic or metabarcoding studies, and highlight inconsistencies in the current freshwater sponge classification.
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Affiliation(s)
- Dirk Erpenbeck
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany
| | - Markus Steiner
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Astrid Schuster
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin J Genner
- c School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Renata Manconi
- d Dipartimento di Medicina Veterinaria, Università di Sassari, Sassari, Italy
| | - Roberto Pronzato
- e Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, Università di Genova, Genova, Italy
| | - Bernhard Ruthensteiner
- b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany.,f SNSB - Bavarian State Collection of Zoology, Munich, Germany
| | | | | | - Gert Wörheide
- a Department of Earth & Environmental Sciences, Palaeontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany.,b GeoBio-CenterLMU, Ludwig-Maximilians-Universität, Munich, Germany.,i Bavarian State Collections of Palaeontology and Geology, Munich, Germany
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Shaffer MR, Davy SK, Bell JJ. Hidden diversity in the genus Tethya: comparing molecular and morphological techniques for species identification. Heredity (Edinb) 2018; 122:354-369. [PMID: 30131516 DOI: 10.1038/s41437-018-0134-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/25/2018] [Accepted: 07/29/2018] [Indexed: 11/09/2022] Open
Abstract
Correctly determining species' identity is critical for estimating biodiversity and effectively managing marine populations, but is difficult for species that have few morphological traits or are highly plastic. Sponges are considered a taxonomically difficult group because they lack multiple consistent diagnostic features, which coupled with their common phenotypic plasticity, makes the presence of species complexes likely, but difficult to detect. Here, we investigated the evolutionary relationship of Tethya spp. in central New Zealand using both molecular and morphological techniques to highlight the potential for cryptic speciation in sponges. Phylogenetic reconstructions based on two mitochondrial markers (rnl, COI-ext) and one nuclear marker (18S) revealed three genetic clades, with one clade representing Tethya bergquistae and two clades belonging to what was a priori thought to be a single species, Tethya burtoni. Eleven microsatellite markers were also used to further resolve the T. burtoni group, revealing a division consistent with the 18S and rnl data. Morphological analysis based on spicule characteristics allowed T. bergquistae to be distinguished from T. burtoni, but revealed no apparent differences between the T. burtoni clades. Here, we highlight hidden genetic diversity within T. burtoni, likely representing a group consisting of incipient species that have undergone speciation but have yet to express clear morphological differences. Our study supports the notion that cryptic speciation in sponges may go undetected and diversity underestimated when using only morphology-based taxonomy, which has broad scale implications for conservation and management of marine systems.
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Affiliation(s)
- Megan R Shaffer
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand.
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
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Uriz MJ, Garate L, Agell G. Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida). PeerJ 2017; 5:e2958. [PMID: 28286707 PMCID: PMC5344016 DOI: 10.7717/peerj.2958] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 01/04/2017] [Indexed: 01/22/2023] Open
Abstract
Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean Hemimycale also suggest that Hemimycale arabica fit in a separate genus. On the other hand, the Atlanto-Mediterranean Crellidae appeared in 18S and 28S phylogenies as a sister group of the Atlanto-Mediterranean Hemimycale. Moreover, what was known up to now as Hemimycale columella, is formed by two cryptic species with contrasting bathymetric distributions. Some small but consistent morphological differences allow species distinction. Conclusions A new family (Hemimycalidae) including the genus Hemimycale and the two purported new genera receiving C. cyathophora and Hemimycale arabica might be proposed according to our phylogenetic results. However, the inclusion of additional Operational Taxonomic Unit (OTUs) appears convenient before taking definite taxonomical decisions. A new cryptic species (Hemimycale mediterranea sp. nov.) is described. Morphologically undifferentiated species with contrasting biological traits, as those here reported, confirm that unidentified cryptic species may confound ecological studies.
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Affiliation(s)
- Maria J Uriz
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
| | - Leire Garate
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
| | - Gemma Agell
- Department of Marine Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC) , Blanes, Girona , Spain
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Yang Q, Franco CMM, Sorokin SJ, Zhang W. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations. Sci Rep 2017; 7:41422. [PMID: 28150727 PMCID: PMC5288722 DOI: 10.1038/srep41422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 01/29/2023] Open
Abstract
For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia
| | - Shirley J Sorokin
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,SARDI Aquatic Sciences, 2 Hamra Ave, West Beach, SA 5024, Australia
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Department of Medical Biotechnology, School of Medicine, Faculty of Medicine, Nursing and Health Sciences, Flinders University, Adelaide, South Australia, SA 5042, Australia.,Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China
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DeBiasse MB, Hellberg ME. Discordance between morphological and molecular species boundaries among Caribbean species of the reef sponge Callyspongia. Ecol Evol 2015; 5:663-75. [PMID: 25691989 PMCID: PMC4328770 DOI: 10.1002/ece3.1381] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/03/2014] [Indexed: 01/29/2023] Open
Abstract
Sponges are among the most species-rich and ecologically important taxa on coral reefs, yet documenting their diversity is difficult due to the simplicity and plasticity of their morphological characters. Genetic attempts to identify species are hampered by the slow rate of mitochondrial sequence evolution characteristic of sponges and some other basal metazoans. Here we determine species boundaries of the Caribbean coral reef sponge genus Callyspongia using a multilocus, model-based approach. Based on sequence data from one mitochondrial (COI), one ribosomal (28S), and two single-copy nuclear protein-coding genes, we found evolutionarily distinct lineages were not concordant with current species designations in Callyspongia. While C. fallax,C. tenerrima, and C. plicifera were reciprocally monophyletic, four taxa with different morphologies (C. armigera,C. longissima,C. eschrichtii, and C. vaginalis) formed a monophyletic group and genetic distances among these taxa overlapped distances within them. A model-based method of species delimitation supported collapsing these four into a single evolutionary lineage. Variation in spicule size among these four taxa was partitioned geographically, not by current species designations, indicating that in Callyspongia, these key taxonomic characters are poor indicators of genetic differentiation. Taken together, our results suggest a complex relationship between morphology and species boundaries in sponges.
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Affiliation(s)
- Melissa B DeBiasse
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
- Correspondence Melissa B DeBiasse, Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803., Tel: 225 578 4284; Fax: 225 578 2597; E-mail:
| | - Michael E Hellberg
- Department of Biological Sciences, Louisiana State University202 Life Sciences Building, Baton Rouge, Louisiana, 70803
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Noyer C, Casamayor EO, Becerro MA. Environmental heterogeneity and microbial inheritance influence sponge-associated bacterial composition of Spongia lamella. MICROBIAL ECOLOGY 2014; 68:611-620. [PMID: 24801965 DOI: 10.1007/s00248-014-0428-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Sponges are important components of marine benthic communities. High microbial abundance sponges host a large diversity of associated microbial assemblages. However, the dynamics of such assemblages are still poorly known. In this study, we investigated whether bacterial assemblages present in Spongia lamella remained constant or changed as a function of the environment and life cycle. Sponges were collected in multiple locations and at different times of the year in the western Mediterranean Sea and in nearby Atlantic Ocean to cover heterogeneous environmental variability. Co-occurring adult sponges and offsprings were compared at two of the sites. To explore the composition and abundance of the main bacteria present in the sponge mesohyl, embryos, and larvae, we applied both 16S rRNA gene-denaturing gradient gel electrophoresis (DGGE) and sequencing of excised DGGE bands and quantitative polymerase chain reactions (qPCR). On average, the overall core bacterial assemblage showed over 60 % similarity. The associated bacterial assemblage fingerprints varied both within and between sponge populations, and the abundance of specific bacterial taxa assessed by qPCR significantly differed among sponge populations and between adult sponge and offsprings (higher proportions of Actinobacteria in the latter). Sequences showed between 92 and 100 % identity to sequences previously reported in GenBank, and all were affiliated with uncultured invertebrate bacterial symbionts (mainly sponges). Sequences were mainly related to Chloroflexi and Acidobacteria and a few to Actinobacteria and Bacteroidetes. Additional populations may have been present under detection limits. Overall, these results support that both ecological and biological sponge features may shape the composition of endobiont bacterial communities in S. lamella.
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Affiliation(s)
- Charlotte Noyer
- Department of Marine Biology, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Accés a la Cala St. Francesc 14, 17300, Blanes, Girona, Spain
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Rubio-Portillo E, Souza-Egipsy V, Ascaso C, de Los Rios Murillo A, Ramos-Esplá AA, Antón J. Eukarya associated with the stony coral Oculina patagonica from the Mediterranean Sea. Mar Genomics 2014; 17:17-23. [PMID: 24950182 DOI: 10.1016/j.margen.2014.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/05/2014] [Accepted: 06/05/2014] [Indexed: 10/25/2022]
Abstract
Oculina patagonica is a putative alien scleractinian coral from the Southwest Atlantic that inhabits across the Mediterranean Sea. Here, we have addressed the diversity of Eukarya associated with this coral and its changes related to the environmental conditions and coral status. A total of 46 colonies of O. patagonica were taken from Alicante coast (Spain) and Pietra Ligure coast (Italy) and analyzed using denaturing gradient gel electrophoresis (DGGE) of the small-subunit 18S rRNA and 16S plastid rRNA genes, internal transcribed spacer region 2 (ITS 2) analyses, and electron microscopy. Our results show that Eukarya and plastid community associated to O. patagonica change with environmental conditions and coral status. Cryptic species, which can be difficult to identify by optical methods, were distinguished by 18S rRNA gene DGGE: the barnacle Megatrema anglicum, which was detected at two locations, and two boring sponges related to Cliona sp. and Siphonodictyon coralliphagum detected in samples from Tabarca and Alicante Harbour, respectively. Eukaryotic phototrophic community from the skeletal matrix of healthy corals was dominated by Ochrosphaera sp. while bleached corals from the Harbour and Tabarca were associated to different uncultured phototrophic organism. Differences in ultrastructural morphologies of the zooxanthellae between healthy and bleached corals were observed. Nevertheless, no differences were found in Symbiodinium community among time, environments, coral status and location, showing that O. patagonica hosted only one genotype of Symbiodinium belonging to clade B2. The fact that this clade has not been previously detected in other Mediterranean corals and is more frequent in the tropical Western Atlantic, is a new evidence that O. patagonica is an alien species in the Mediterranean Sea.
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Affiliation(s)
- Esther Rubio-Portillo
- Dpto. Ciencias del Mar y Biología Aplicada, Universidad de Alicante, 03080 Alicante, Spain.
| | - Virginia Souza-Egipsy
- Servicio de Microscopía Electrónica, Instituto de Ciencias Agrarias-CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | - Carmen Ascaso
- Dpto Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales-CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | - Asunción de Los Rios Murillo
- Dpto Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales-CSIC, Serrano 115 bis, 28006 Madrid, Spain
| | - Alfonso A Ramos-Esplá
- Dpto. Ciencias del Mar y Biología Aplicada, Universidad de Alicante, 03080 Alicante, Spain; Centro de Investigación Marina (CIMAR), Universidad de Alicante-Ayuntamiento de Santa Pola, Cabo de Santa Pola s/n, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, 03080 Alicante, Spain
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Cruz-Barraza JA, Vega C, Carballo JL. Taxonomy of family Plakinidae (Porifera: Homoscleromorpha) from eastern Pacific coral reefs, through morphology andcox1andcob mtDNA data. Zool J Linn Soc 2014. [DOI: 10.1111/zoj.12137] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Antonio Cruz-Barraza
- Instituto de Ciencias del Mar y Limnología; Universidad Nacional Autónoma de México (Unidad Académica Mazatlán); Avenida Joel Montes Camarena s/n, PO box 811 Mazatlán SIN 82000 México
| | - Cristina Vega
- Instituto de Ciencias del Mar y Limnología; Universidad Nacional Autónoma de México (Unidad Académica Mazatlán); Avenida Joel Montes Camarena s/n, PO box 811 Mazatlán SIN 82000 México
| | - José Luis Carballo
- Instituto de Ciencias del Mar y Limnología; Universidad Nacional Autónoma de México (Unidad Académica Mazatlán); Avenida Joel Montes Camarena s/n, PO box 811 Mazatlán SIN 82000 México
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Abdul Wahab M, Fromont J, Whalan S, Webster N, Andreakis N. Combining morphometrics with molecular taxonomy: How different are similar foliose keratose sponges from the Australian tropics? Mol Phylogenet Evol 2014; 73:23-39. [DOI: 10.1016/j.ympev.2014.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 11/22/2013] [Accepted: 01/03/2014] [Indexed: 10/25/2022]
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14
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Gazave E, Lavrov DV, Cabrol J, Renard E, Rocher C, Vacelet J, Adamska M, Borchiellini C, Ereskovsky AV. Systematics and molecular phylogeny of the family oscarellidae (homoscleromorpha) with description of two new oscarella species. PLoS One 2013; 8:e63976. [PMID: 23737959 PMCID: PMC3667853 DOI: 10.1371/journal.pone.0063976] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 04/06/2013] [Indexed: 11/19/2022] Open
Abstract
The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups.
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Affiliation(s)
- Eve Gazave
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
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15
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Boury-Esnault N, Lavrov DV, Ruiz CA, Pérez T. The integrative taxonomic approach applied to porifera: a case study of the homoscleromorpha. Integr Comp Biol 2013; 53:416-27. [PMID: 23670632 DOI: 10.1093/icb/ict042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The two main scientific tasks of taxonomy are species' delineation and classification. These two tasks are often treated differently, with classification accomplished by newly-developed phylogenetic methods, often based on molecular sequences, while delimitation of species is conducted by what is often considered to be an "old-fashioned" typological approach based on morphological description. A new "integrative taxonomy" has been proposed which maintains that species delimitation should be a multidisciplinary undertaking combining several independent datasets. Here we argue that the same principle is relevant to the classification of species. In the past 20 years, we assembled various datasets based on the external morphology, anatomy, cytology, spicule shapes, geography, reproduction, genetic sequences, and metabolomics of homoscleromorph sponges. We show how we used these datasets to describe new species of homoscleromorph sponges and to elucidate their phylogenetic relationships and their phylogenetic position within the phylum Porifera.
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Affiliation(s)
- Nicole Boury-Esnault
- *IMBE-UMR7263 CNRS, Université d'Aix-Marseille, Station Marine d'Endoume, Marseille, France; Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
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16
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Arunachalam R. Detection of site-specific positive Darwinian selection on pandemic influenza A/H1N1 virus genome: integrative approaches. Genetica 2013; 141:143-55. [DOI: 10.1007/s10709-013-9713-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/18/2013] [Indexed: 12/17/2022]
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17
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Abstract
Knowledge of the functioning, health state, and capacity for recovery of marine benthic organisms and assemblages has become essential to adequately manage and preserve marine biodiversity. Molecular tools have allowed an entirely new way to tackle old and new questions in conservation biology and ecology, and sponge science is following this lead. In this review, we discuss the biological and ecological studies of sponges that have used molecular markers during the past 20 years and present an outlook for expected trends in the molecular ecology of sponges in the near future. We go from (1) the interface between inter- and intraspecies studies, to (2) phylogeography and population level analyses, (3) intra-population features such as clonality and chimerism, and (4) environmentally modulated gene expression. A range of molecular markers has been assayed with contrasting success to reveal cryptic species and to assess the genetic diversity and connectivity of sponge populations, as well as their capacity to respond to environmental changes. We discuss the pros and cons of the molecular gene partitions used to date and the prospects of a plentiful supply of new markers for sponge ecological studies in the near future, in light of recently available molecular technologies. We predict that molecular ecology studies of sponges will move from genetics (the use of one or some genes) to genomics (extensive genome or transcriptome sequencing) in the forthcoming years and that sponge ecologists will take advantage of this research trend to answer ecological and biological questions that would have been impossible to address a few years ago.
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Affiliation(s)
- Maria J Uriz
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Blanes, Girona, Spain.
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18
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Wulff J. Ecological interactions and the distribution, abundance, and diversity of sponges. ADVANCES IN MARINE BIOLOGY 2012; 61:273-344. [PMID: 22560780 DOI: 10.1016/b978-0-12-387787-1.00003-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Although abiotic factors may be important first-order filters dictating which sponge species can thrive at a particular site, ecological interactions can play substantial roles influencing distribution and abundance, and thus diversity. Ecological interactions can modify the influences of abiotic factors both by further constraining distribution and abundance due to competitive or predatory interactions and by expanding habitat distribution or abundance due to beneficial interactions that ameliorate otherwise limiting circumstances. It is likely that the importance of ecological interactions has been greatly underestimated because they tend to only be revealed by experiments and time-series observations in the field. Experiments have revealed opportunistic predation to be a primary enforcer of sponge distribution boundaries that coincide with habitat boundaries in several systems. Within habitats, by contrast, dramatic effects of predators on sponge populations seem to occur primarily in cases of unusually high recruitment rates or unusually low mortality rates for the predators, which are often specialists on the sponge species affected. Competitive interactions have been demonstrated to diminish populations or exclude sponge species from a habitat in only a few cases. Cases in which competitive interactions have appeared obvious have often turned out to be neutral or even beneficial interactions when observed over time. Especially striking in this regard are sponge-sponge interactions in dense sponge-dominated communities, which may promote the continued coexistence of all participating species. Mutualistic symbioses of sponges with other animals, plants, or macroalgae have been demonstrated to increase abundance, habitat distribution, and diversity of all participants. Symbiotic microbes can enhance sponge distribution and abundance but also render their hosts more vulnerable to environmental changes. And while photosynthetic symbionts can boost growth and excavation rates for some sponge hosts, in other cases sponge growth proceeds as well or even better in diminished light. Metrics chosen for evaluating sponge abundance make a substantial difference in interpretation of data comparing between different sites, or over time at the same site. In most cases, evaluating abundance by volume or biomass allows more ecologically meaningful interpretation of influences on distribution and abundance than does evaluating abundance by numbers of individuals or area covered. Accurate identification of species, and understanding how they are related within higher taxa, is essential. Studies in every habitat have illustrated the great power of experimental manipulations, and of time-series observations of sponge individuals, for understanding the processes underlying observed patterns; in many cases, these processes have been revealed to be ecological interactions.
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Affiliation(s)
- Janie Wulff
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
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Cárdenas P, Pérez T, Boury-Esnault N. Sponge systematics facing new challenges. ADVANCES IN MARINE BIOLOGY 2012; 61:79-209. [PMID: 22560778 DOI: 10.1016/b978-0-12-387787-1.00010-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Systematics is nowadays facing new challenges with the introduction of new concepts and new techniques. Compared to most other phyla, phylogenetic relationships among sponges are still largely unresolved. In the past 10 years, the classical taxonomy has been completely overturned and a review of the state of the art appears necessary. The field of taxonomy remains a prominent discipline of sponge research and studies related to sponge systematics were in greater number in the Eighth World Sponge Conference (Girona, Spain, September 2010) than in any previous world sponge conferences. To understand the state of this rapidly growing field, this chapter proposes to review studies, mainly from the past decade, in sponge taxonomy, nomenclature and phylogeny. In a first part, we analyse the reasons of the current success of this field. In a second part, we establish the current sponge systematics theoretical framework, with the use of (1) cladistics, (2) different codes of nomenclature (PhyloCode vs. Linnaean system) and (3) integrative taxonomy. Sponges are infamous for their lack of characters. However, by listing and discussing in a third part all characters available to taxonomists, we show how diverse characters are and that new ones are being used and tested, while old ones should be revisited. We then review the systematics of the four main classes of sponges (Hexactinellida, Calcispongiae, Homoscleromorpha and Demospongiae), each time focusing on current issues and case studies. We present a review of the taxonomic changes since the publication of the Systema Porifera (2002), and point to problems a sponge taxonomist is still faced with nowadays. To conclude, we make a series of proposals for the future of sponge systematics. In the light of recent studies, we establish a series of taxonomic changes that the sponge community may be ready to accept. We also propose a series of sponge new names and definitions following the PhyloCode. The issue of phantom species (potential new species revealed by molecular studies) is raised, and we show how they could be dealt with. Finally, we present a general strategy to help us succeed in building a Porifera tree along with the corresponding revised Porifera classification.
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Affiliation(s)
- P Cárdenas
- Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle, UMR 7208 "BOrEA", Paris, France
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20
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de Paula TS, Zilberberg C, Hajdu E, Lôbo-Hajdu G. Morphology and molecules on opposite sides of the diversity gradient: Four cryptic species of the Cliona celata (Porifera, Demospongiae) complex in South America revealed by mitochondrial and nuclear markers. Mol Phylogenet Evol 2012; 62:529-41. [DOI: 10.1016/j.ympev.2011.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 09/20/2011] [Accepted: 11/03/2011] [Indexed: 11/30/2022]
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21
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DAILIANIS T, TSIGENOPOULOS CS, DOUNAS C, VOULTSIADOU E. Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation. Mol Ecol 2011; 20:3757-72. [DOI: 10.1111/j.1365-294x.2011.05222.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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22
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Reveillaud J, van Soest R, Derycke S, Picton B, Rigaux A, Vanreusel A. Phylogenetic relationships among NE Atlantic Plocamionida Topsent (1927) (Porifera, Poecilosclerida): under-estimated diversity in reef ecosystems. PLoS One 2011; 6:e16533. [PMID: 21347368 PMCID: PMC3036665 DOI: 10.1371/journal.pone.0016533] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 12/20/2010] [Indexed: 11/23/2022] Open
Abstract
Background Small and cryptic sponges associated with cold-water coral reefs are particularly numerous and challenging to identify, but their ecological and biochemical importance is likely to compete with megabenthic specimens. Methodology/Principal Findings Here we use a combination of the standard M1M6 and I3M11 partitions of the COI fragment, partial rDNA 28S sequences and morphology to delineate small encrusting Plocamionida species. In total, 46 specimens were retrieved from seven shallow to deep-water coral locations, crossing 3,000 km along the European margins. Our work provides evidence that the Plocamionida ambigua f. tylotata and f. grandichelata can be considered valid species, whereas Plocamionida ambigua f. tornata corresponds to the species P. ambigua. Within the monophyletic group of Plocamionida, P. microcionides is shown as really divergent from the other taxa, and four putative new Plocamionida species are suggested. Conclusions/Significance This study shows that the use of molecular and morphological information in an integrative approach is a powerful tool for the identification of sponge species, and suggests that an under-estimated biodiversity of sponges occurs in cold-water coral reefs.
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Affiliation(s)
- Julie Reveillaud
- Marine Biology Section, Biology Department, Ghent University, Ghent, Belgium.
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23
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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24
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Gazave E, Carteron S, Chenuil A, Richelle-Maurer E, Boury-Esnault N, Borchiellini C. Polyphyly of the genus Axinella and of the family Axinellidae (Porifera: Demospongiaep). Mol Phylogenet Evol 2010; 57:35-47. [DOI: 10.1016/j.ympev.2010.05.028] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 05/20/2010] [Accepted: 05/31/2010] [Indexed: 10/19/2022]
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25
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Do bipolar distributions exist in marine sponges? Stylocordyla chupachups sp. nv. (Porifera: Hadromerida) from the Weddell Sea (Antarctic), previously reported as S. borealis (Lovén, 1868). Polar Biol 2010. [DOI: 10.1007/s00300-010-0876-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Phylogenetic inference of Indian malaria vectors from multilocus DNA sequences. INFECTION GENETICS AND EVOLUTION 2010; 10:755-63. [DOI: 10.1016/j.meegid.2010.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Revised: 04/22/2010] [Accepted: 04/22/2010] [Indexed: 02/02/2023]
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27
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Xavier JR, Rachello-Dolmen PG, Parra-Velandia F, Schönberg CHL, Breeuwer JAJ, van Soest RWM. Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae). Mol Phylogenet Evol 2010; 56:13-20. [PMID: 20363344 DOI: 10.1016/j.ympev.2010.03.030] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 03/02/2010] [Accepted: 03/29/2010] [Indexed: 12/01/2022]
Affiliation(s)
- J R Xavier
- Evolutionary Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam (IBED), Amsterdam, The Netherlands.
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28
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Reveillaud J, Remerie T, van Soest R, Erpenbeck D, Cárdenas P, Derycke S, Xavier JR, Rigaux A, Vanreusel A. Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae). Mol Phylogenet Evol 2010; 56:104-14. [PMID: 20382244 DOI: 10.1016/j.ympev.2010.03.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 02/24/2010] [Accepted: 03/29/2010] [Indexed: 11/16/2022]
Abstract
Coral reefs constitute the most diverse ecosystem of the marine realm and an increasing number of studies are focusing on coral species boundaries, distribution, and on processes that control species ranges. However, less attention has been paid to coral associated species. Deep-sea sponges dominate cold-water coral ecosystems, but virtually nothing is known about their molecular diversity. Moreover, species boundaries based on morphology may sometimes be inadequate, since sponges have few diagnostic characters. In this study, we investigated the molecular diversity within the genus Hexadella (Porifera, Demospongiae, Verongida, Ianthellidae) from the European shallow-water environment to the deep-sea coral ecosystems. Three molecular markers were used: one mitochondrial (COI) and two nuclear gene fragments (28S rDNA and the ATPS intron). Phylogenetic analyses revealed deeply divergent deep-sea clades congruent across the mitochondrial and nuclear markers. One clade contained specimens from the Irish, the Scottish, and the Norwegian margins and the Greenland Sea (Hexadella dedritifera) while another clade contained specimens from the Ionian Sea, the Bay of Biscay, and the Irish margin (H. cf. dedritifera). Moreover, these deeply divergent deep-sea clades showed a wide distribution suggesting a connection between the reefs. The results also point to the existence of a new deep-sea species (Hexadella sp.) in the Mediterranean Sea and of a cryptic shallow-water species (Hexadella cf. pruvoti) in the Gorringe Bank. In contrast, low genetic differentiation between H. cf. dedritifera and H. pruvoti from the Mediterranean Sea was observed. All Hexadella racovitzai specimens from the Mediterranean Sea (shallow and deep) to the Atlantic formed a monophyletic group.
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Pöppe J, Sutcliffe P, Hooper JNA, Wörheide G, Erpenbeck D. CO I barcoding reveals new clades and radiation patterns of Indo-Pacific sponges of the family Irciniidae (Demospongiae: Dictyoceratida). PLoS One 2010; 5:e9950. [PMID: 20376349 PMCID: PMC2848591 DOI: 10.1371/journal.pone.0009950] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 09/28/2009] [Indexed: 11/18/2022] Open
Abstract
Background DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance. Methodology/Principal Findings Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates. Conclusions/Significance We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.
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Affiliation(s)
- Judith Pöppe
- Museum für Naturkunde, Department of Malacozoology, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Berlin, Germany
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30
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Harcet M, Bilandžija H, Bruvo-Mađarić B, Ćetković H. Taxonomic position of Eunapius subterraneus (Porifera, Spongillidae) inferred from molecular data – A revised classification needed? Mol Phylogenet Evol 2010; 54:1021-7. [DOI: 10.1016/j.ympev.2009.12.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 12/03/2009] [Accepted: 12/21/2009] [Indexed: 11/29/2022]
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31
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Blanquer A, Uriz MJ. Population genetics at three spatial scales of a rare sponge living in fragmented habitats. BMC Evol Biol 2010; 10:13. [PMID: 20074333 PMCID: PMC2818636 DOI: 10.1186/1471-2148-10-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 01/14/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rare species have seldom been studied in marine habitats, mainly because it is difficult to formally assess the status of rare species, especially in patchy benthic organisms, for which samplings are often assumed to be incomplete and, thus, inappropriate for establishing the real abundance of the species. However, many marine benthic invertebrates can be considered rare, due to the fragmentation and rarity of suitable habitats. Consequently, studies on the genetic connectivity of rare species in fragmented habitats are basic for assessing their risk of extinction, especially in the context of increased habitat fragmentation by human activities. Sponges are suitable models for studying the intra- and inter-population genetic variation of rare invertebrates, as they produce lecitotrophic larvae and are often found in fragmented habitats. RESULTS We investigated the genetic structure of a Mediterranean sponge, Scopalina lophyropoda (Schmidt), using the allelic size variation of seven specific microsatellite loci. The species can be classified as "rare" because of its strict habitat requirements, the low number of individuals per population, and the relatively small size of its distribution range. It also presents a strong patchy distribution, philopatric larval dispersal, and both sexual and asexual reproduction. Classical genetic-variance-based methods (AMOVA) and differentiation statistics revealed that the genetic diversity of S. lophyropoda was structured at the three spatial scales studied: within populations, between populations of a geographic region, and between isolated geographic regions, although some stochastic gene flow might occur among populations within a region. The genetic structure followed an isolation-by-distance pattern according to the Mantel test. However, despite philopatric larval dispersal and fission events in the species, no single population showed inbreeding, and the contribution of clonality to the population makeup was minor (only ca. 4%). CONCLUSIONS The structure of the S. lophyropoda populations at all spatial scales examined confirms the philopatric larval dispersal that has been reported. Asexual reproduction does not seem to play a relevant role in the populations. The heterozygote excess and the lack of inbreeding could be interpreted as a hitherto unknown outcrossing strategy of the species. The envisaged causes for this strategy are sperm dispersal, a strong selection against the mating of genetically related individuals to avoid inbreeding depression or high longevity of genets combined with stochastic recruitment events by larvae from other populations. It should be investigated whether this strategy could also explain the genetic diversity of many other patchy marine invertebrates whose populations remain healthy over time, despite their apparent rarity.
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Affiliation(s)
- Andrea Blanquer
- Departament d'Ecologia Marina, Centre d'Estudis Avançats de Blanes, CSIC, Accés Cala St Francesc 14, 17300 Blanes, Girona, Spain.
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CABEZAS PATRICIA, MACPHERSON ENRIQUE, MACHORDOM ANNIE. Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South-West Pacific). Zool J Linn Soc 2009. [DOI: 10.1111/j.1096-3642.2008.00492.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Blanquer A, Uriz MJ. 'A posteriori' searching for phenotypic characters to describe new cryptic species of sponges revealed by molecular markers (Dictyonellidae : Scopalina). INVERTEBR SYST 2008. [DOI: 10.1071/is07004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cryptic speciation is repeatedly reported in sponge taxonomic studies. Most of the cryptic species, which were revealed by molecular markers, have never been formally described owing to the difficulty in finding diagnostic phenotypic characters. A previous molecular study revealed four genetically distinct species that had been misidentified as Scopalina lophyropoda Schmidt. One species was S. lophyropoda sensu stricto, whereas the other three were new species. Here, the three new species are formally described after careful searching for discriminatory phenotypic characters. The new species are Scopalina blanensis, sp. nov. from the north-western Mediterranean, S. ceutensis, sp. nov. from the Mediterranean coasts of Africa (Atlantic waters) and S. canariensis, sp. nov. from the Canary Islands, Atlantic Ocean. All of them are at first sight morphologically similar and inhabit shallow environments with resuspended sediment. However, a closer examination allowed us to find some differential features: e.g. the amount of spongin embedding the spicules, the degree of complexity of the skeletal tracts, the size and curvature of the styles, the growth habit and the colour tinge. Furthermore, an identification key to the Atlanto-Mediterranean Scopalina species is presented. The differences between the genera Scopalina, Ulosa and Dictyonella are also discussed.
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