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.
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.
Citation: Reveillaud J, van Soest R, Derycke S, Picton B, Rigaux A, Vanreusel A (2011) Phylogenetic Relationships among NE Atlantic Plocamionida Topsent (1927) (Porifera, Poecilosclerida): Under-Estimated Diversity in Reef Ecosystems. PLoS ONE6(2): e16533. https://doi.org/10.1371/journal.pone.0016533
Editor: Vincent Laudet, Ecole Normale Supérieure de Lyon, France
Received: September 3, 2010; Accepted: December 20, 2010; Published: February 9, 2011
Copyright: © 2011 Reveillaud et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: The support of a SYNTHESYS Grant financed by European Community Research Infrastructure Action under the FP6 "Structuring the European Research Area" Program to visit to the Zoological Museum in Amsterdam (JR) is acknowledged. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007–2013) under the HERMIONE project, grant 517 agreement n° 226354. JR had a Special Research Fund (BOF) from Ghent University. The study benefited from funding by the EUROMARGIN Programme of the European Science Foundation (Moundforce 2004 Project, 813.03.006/855.01.040) and the Netherlands Organisation for Scientific Research (BIOSYS project 814.01.005/835.20.024) to support sponge material collection. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Sponges represent one of the most remarkable groups in deep-water coral ecosystems , . The high biodiversity and abundance of these filter-feeders (with a total of 191 species recorded in Irish bathyal coral reefs, ) contrasts with the paucity of the coral reef building species, predominantly Lophelia pertusa (Linnaeus 1758) and Madrepora oculata (Linnaeus 1758). Ecologists initially focused on large-sized, bright-coloured or conspicuous Porifera species (e.g. –), but the extensive presence of small sized and morphologically cryptic sponges in cold-water coral reefs (CWRs) has widely been noted , –. Single dead coral branches from cold waters can contain up to 15 sponge species . The distribution of CWRs along the European margins has now been well documented , and several coral hotspots are found along the continental margin off Ireland, off Norway, and in the Mediterranean basin. Nevertheless, only few biodiversity studies have addressed the substantial diversity of deep-sea sponges associated with CWRs , –. Such lack of knowledge forms a substantial impediment for establishing baselines of biodiversity and for the efficient management of this group , which is of particular interest for the pharmaceutical industry . Moreover, the significance of these deep and nutrient rich hotspot ecosystems for potential centers of endemism has direct implications for both regional diversity and local endemicity.
The sponge genus Plocamionida Topsent (1927) (Class Demospongiae, Order Poecilosclerida, Family Hymedesmiidae) is widely distributed along the continental margins of Europe, and occurs from the Mediterranean Sea and the Azores to “high latitudes” in the NE Atlantic , –. Within CWR environments, Plocamionida species encrust rocks or hard corals in thin (<5 mm) sheets of brown coloration and can be locally abundant. Occasionally, shallow-water occurrence is reported, but their main occurrence is at depths of 50 m and deeper. Although the genus has excellent morphological markers, the taxonomic distinctness of its European species remains highly contentious. Two species names, P. ambigua (Bowerbank, 1866) and P. microcionides (Carter, 1876) have been considered as valid separate species, or as synonyms of a single variable species (e.g. , ). Furthermore, a number of ‘formas’ have been proposed by various authors for specimens with deviating spicule characteristics, Plocamionida microcionides f. achelata Topsent, 1928, Plocamionida ambigua f. grandichelata Brøndsted, 1932, Plocamionida ambigua f. tornotata Brøndsted, 1932 and Plocamionida ambigua f. tylotata Brøndsted, 1932. The latter form has been given species status by Alander  and Picton and Goodwin . Plocamionida remains a group of sponges that are notoriously difficult to identify because the intra- and interspecific character variation is not well understood, and has given rise to disagreements between taxonomic experts.
The first aim of this study is to investigate the phylogenetic relationships of Plocamionida species and formas from the Gulf of Cadiz to Norway occurring in CWRs. Specimens from one shallow water population were also included. We used phylogenetic congruence criteria between the cytochrome oxidase c subunit I (COI) and the independent nuclear region D3–D5 of the rDNA 28S gene to delineate evolutionary significant units, and to reveal the presence of cryptic species within the studied material. The standard (COI) barcoding fragment, amplified with the universal primers of Folmer et al. (; hereafter called the M1M6 partition) is generally too conserved in diploblast phyla  and has led to some difficulties in resolving taxonomic and phylogeographic relationships in sponges , . On the other hand, genetic studies above and below the species level have been performed using this COI partition , –. In addition, the COI downstream I3M11 partition showed more resolution than the standard M1M6 partition . It proved useful at interspecific level  and to determine the genetic population structure of Caribbean and European sponge species , . Herein, we seize the opportunity to compare the I3M11 partition to the M1M6 partition in terms of amplification success and substitution pattern, as well as to assess the potential of their combination for species level delineation. Second, the phylogenetic units were morphologically analyzed to investigate whether concordant molecular lineages are also morphologically distinct and to resolve the current taxonomic difficulties in Plocamionida.
Materials and Methods
A total of 46 specimens of Plocamionida were collected from seven locations along the Atlantic continental margin spanning about 3,000 km (Fig. 1). Normal storm waves disturb the seafloor significantly down to 50 m  and this depth was used to separate shallow from deep-water environments. Deep-water specimens (>50 m) were collected with boxcores or with a Remote Operated Vehicle (ROV) during five cruises and one specimen was dredged up from the coast of Norway in Bergen (Table S1). Shallow-water specimens were collected by scuba diving at The Maidens, Northern Ireland. Specimens were detected by searching dead coral branches and stones using a low power microscope. All samples were preserved in absolute ethanol and stored at room temperature until further processing. Plocamionida-like individuals were identified by looking at their skeletal structure using thick sections air-dried on microscopical slides and mounted in Canada balsam. Voucher specimens are deposited in the Porifera collection of the Zoological Museum of Amsterdam (ZMAPOR) and in the Ulster Museum, Belfast (BELUM) and are available upon request. The list of studied species and localities with their abbreviations is given in Table S1.
Map was provided by the project Hotspot Ecosystem Research and Man's Impact on European Seas (HERMIONE). Sampling location are given in uppercase letters for deep-water samples (>50 m) and in lowercase letters for shallow-water samples.
DNA extraction, PCR setup and amplifications
DNA extraction from samples was performed using the DNeasy Blood and Tissue Kit (Qiagen) in accordance with the manufacturer's instructions. Polymerase chain reaction (PCR) amplifications were carried out in a total volume of 47 µl, with 5 µl of 10 x PCR buffer (Qiagen), 5 µl of 10x CoralLoad (Qiagen), 1 µl MgCl2 (25 mM), 1 µl dNTP (10 mM each), 0.5 µl of BSA (10 µg/µl), 1 µl of forward and reverse primer (25 µM), 0.25 µl TopTaq DNA polymerase (5 u/µl, Qiagen), 1 µl of template DNA and 31.25 µl of HPLC grade water.
A∼1200 bp long fragment of the cytochrome c oxidase subunit I (COI) mtDNA gene was initially amplified from ten random specimens using the universal primer LCO1490  and the reverse primer COX1-R1 (5′-TGTTGRGGGAAAAARGTTAAATT -3′) . Polymerase chain reaction (PCR) cycling conditions included an initial denaturation step of 5 min at 94°C, 5 cycles (94°C for 1 min, 48°C for 1 min and 72°C for 1 min 30), 30 cycles (94°C for 1 min, 50°C for 1 min and 72°C for 1 min 30) and a final extension at 72°C for 10 min. Based on these ten sequences, specific Plocamionida sp. primer COIPlo20F (5′-GCTTTTGCGGGGATGATAGGTAC-3′) and COI800Rev (5′-TCTACATCCATTCCTACTGTAAACATGTG -3′) were developed to amplify the M1M6 partition () under a temperature regime of 5 min at 94°C followed by 35 cycles of 94°C for 45 s, 47°C for 45 s, 72°C for 45 s and a final extension at 72°C for 10 min. PCR amplifications of the I3M11 partition were performed using the primers COI800Fwd (5′- CACATGTTTACAGTAGGAATGGATGTAGA-3′) (reverse complement from the specific primer COI800Rev) and COX1-R1 under a temperature regime of 94°C for 2 min, followed by 30 cycles of (94°C for 30 s, 47°C for 30 s, 72°C for 30 s) and a final extension at 72°C for 10 min.
The D3–D5 fragment of the rDNA 28S gene fragment was amplified using the primers RD3A 5′-GAC CCG TCT TGA AAC ACG A-3′ and RD5B2 5′- ACA CAC TCC TTA GCG GA-3′  under a temperature regime described in Reveillaud et al. .
PCR product processing and sequencing
The PCR-amplified products were loaded onto a 1% agarose gel, checked for size, and sequenced in both directions through a Perkin- 234 Elmer ABI 3130 capillary DNA sequencer. The PCR products were purified by incubation at 37°C using exonuclease I, E. coli (20 U µl−1; Fermentas) and FastAP thermosensitive alkaline phosphatase (1 U µl−1; Fermentas), and labelled using the Big Dye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems). Chromatograms obtained from the automated sequencer were read and contigs assembled using the sequence editing software SeqMan Pro v.7.1.0 (DNASTAR Lasergene). We checked the poriferan origin of the sequences by BLAST searches against the Genbank database (http://www.ncbi.nlm.nih.gov/BLAST/) and their relationship to other taxa in a phylogenetic tree as described in Erpenbeck et al. . All the sequences are deposited in the European Molecular Biology Laboratory (EMBL) under accession numbers FR687219–687251.
Sequence alignment and phylogenetic analyses
COI and 28S sequences were aligned using the web interface of the multiple alignment software MAFFT (; available at http://www.ebi.ac.uk/Tools/mafft/index.html), under default settings. Ambiguous positions in the D3–D5 region of 28S were discarded. Our own sequences of the poecilosclerid sponges Desmacella inornata (Family Desmacellidae) and Mycale lingua (Family Mycalidae) were used as uniform outgroup for all analyses.
Both partitions of the COI gene were combined for phylogenetic analyses. The COI and the 28S partitions were separately analyzed and then combined for the same set of specimens whenever possible. A partition homogeneity test performed in PAUP* 4.0b10  with 100 replicates between the COI and the 28S datasets showed that data partitions were not significantly incongruent (p = 1). Phylogenetic reconstructions of the nucleotide data sets were performed using the maximum likelihood (ML) criterion of PAUP* 4.0b10  and Bayesian inference (BI) criterion of MrBayes 3.1.2 . We used Modeltest 3.06  as well as its simplified version MrModeltest 1.1  to estimate the best-fitting nucleotide model under the Akaike Information Criterion (AIC) for each independent gene for the ML and the BI analysis respectively. The GTR+I best fitted the COI data set for both ML and BI reconstructions whereas for the 28S dataset, the models selected by AIC were TrN+I for the ML reconstructions and HKY+I for the BI analyses. The GTR+G+I model was selected for ML and BI for the combined COI and 28S dataset. ML trees were calculated using heuristic searches and a tree bisection and reconnection (TBR) branch swapping algorithm (10 000 rearrangements), and a random stepwise addition of sequences in 100 replicate trials. Nodal support was estimated with a bootstrap procedure with 100 replications and 10 replicate trials of sequence addition. Bootstrap supports (BS)>70 were considered high enough to support clades in ML reconstructions. Bayesian inference analyses were performed with four Markov-chains for each gene. For COI and the combined COI-28S dataset, analyses were performed with 1 million generations sampled every 1000 generations while 300000 generations sampled every 300 generations were used for the 28S dataset. After all analyses, the average standard deviation of split frequencies was below 0.01. We used the burn-in value of 25%. In BI reconstructions, posterior probabilities (PP)>95 were considered to support clades.
Maximum intraclade (whenever more than one haplotype was found) and minimum interclade/branch corrected p-distances were calculated for the COI and the 28S gene fragment using PAUP* 4.0b10  under the respective models from the ML analyses.
Microscopic examination of spicule ornamentations and measurements of spicule micrometries were done using a compound Leitz microscope at 10×10× and 10×40× magnifications, on dissociated spicule mounts obtained after boiling a fragment in concentrated nitric acid, mounted in Canada balsam. All specimens were examined and classified using the following morphological criteria: presence or absence of spines on the blunt ends of the choanosomal large styles, the tylote, mucronate or pointed shape of the tornote endings, the simple or compound shape of the spines in the acanthostrongyles, and size of the chelae (more or less than 30 microns). For the latter character, at least 25 chelae spicules were measured in each preparation and no overlap was found between the ranges 15–25 versus 30+ µm.
mtDNA COI dataset.
The resulting data sets comprised 27 specimens and 12 haplotypes with 777 characters (88 parsimony informative, ts/tv ratio = 1.941) for the M1M6 partition and 46 specimens, 13 haplotypes with 363 nucleotides (53 parsimony informative, ts/tv ratio = 1.65) for the I3M11 partition (Table S1). Both partitions could unambiguously be aligned and translated into respectively a functional 259 and 121 amino-acid protein sequence of the COI. No frame shifts or point mutations were present. The success rate of the COI amplification in all specimens varied along the COI fragment, with 58% in the M1M6 partition and 85% in the I3M11 partition. The combined dataset contained only specimens from which both partitions were obtained. It comprised 27 specimens and 12 haplotypes with 1140 characters (138 parsimony informative, ts/tv ratio = 1.685) and was used for the phylogenetic reconstruction of the COI gene (Fig. 2).
Bayesian posterior probabilities (when >0.95) and the ML bootstrap values (when >70) are indicated above and below branches, respectively. For information on the specimens (listed in parenthesis) see Table S1.
Plocamionida specimens formed a well supported monophyletic group, with high Bayesian PP and ML BS (1.0/100). The COI tree was divided into two well supported parts A and B (1.0/100) separated by high genetic divergence values (GTR+I corrected p-distance of 14.5% to 20%, Table 1). Part A showed six highly divergent haplotypes (H1–H6) with GTR+I corrected p-distance ranging from 1.3 to 5.9%. H4 and H5 were more closely related to each other than to any of the other sequences. In addition H4–6 and H2–6 formed well supported subclades (1.0/81 and 0.95/92 respectively). Genetic divergence between the six sequences of Part B was much lower (0.5% to 1.9%) than those within part A. Part B was substructured into a well supported clade (H8a–e; 1.0/86) and a highly divergent single sequence (H7). The sequences H8d–e were found to be more closely related to each other than to the other H8 haplotypes.
rDNA 28S dataset.
The resulting data sets comprised 39 specimens and 8 genotypes with 620 nucleotides (15 parsimony informative). Phylogenetic relationships using the 28S fragment were highly similar to the ones obtained from COI, but received less support (Fig. 3): Plocamionida specimens were recovered as a monophyletic group (-/71) and the deeper parts A and B were recovered (-/85 and 1.0/87, respectively). The subclades H4–5 and H4–6 were recovered with high support (0.99/70 and 1.0/79, respectively).The different haplotypes identified in COI as H8a–e shared a single 28S sequence (H8), with a sequence divergence of 0.1% from H7 (Table 2).
Bayesian posterior probabilities (when >0.95) and the ML bootstrap values (when >70) are indicated above and below branches, respectively. For information on the specimens (listed in parenthesis) see Table S1.
Sequence divergence ranged from 1.9 to 3.3% between part A and B, and was 1.2% and 0.1% within Part A and B, respectively (Table 2).
Combined dataset COI-28S.
The concatenated COI-28S dataset comprised 24 specimens with 1760 characters. The monophyly of the Plocamionida specimens was highly supported (1.0/92), and Parts A and B were again recovered with high support (1.0/94 and 1.0/100, respectively; Fig. 4). H4 and H5 were found more closely related to each other as found in COI and subclades H4–6 and H2–6 were highly supported (1.0/98 and 0.97/81 respectively). Subclade H8a–e within part B was recovered with high support (1.0/96) and H8d–e were found to be more closely related to each other, as previously found in COI. Based on the phylogenetic congruence between COI and 28S and the higher genetic divergence value between than within H1–8 in both genes, we consider hereafter H1–8 as independent Evolutionarily Significant Units (ESU).
Most ESUs were characterized by morphological differences, except H1–H3 and H7–H8 (Table 3). Specimens from H6 were characterized by spined large styles, tylote tornotes, a simple shape of the spines in the acanthostrongyle and the size of the chela being smaller than 30 microns (µm). In contrast, H4 and H5 specimens were characterized by a mucronate shape of the tornote endings. The size of the chela further differentiated H4 and H5 specimens. As mentioned above, the three Gulf of Cadiz specimens (H1, H2 and H3) were morphologically similar and possessed the tylote tornotes in combination with a large chela >30 µm. Part B specimens possessed smooth large styles, fusiform tornotes, a truncate shape of the spines in the acanthostrongyle and a chela smaller than 30 µm. The only exception was H8e (P6) from the Gulf of Cadiz which had a chela >30 µm.
Integrative Taxonomy in Plocamionida
The genetic results conform well to previous morphological proposals for the subdivision of Plocamionida into several distinct European taxa. The specimens are divided into eight ESUs, which were grouped into two clades: Part A (H1–6) and part B (H7–8) specimens were separated by high divergence values in the COI and 28S fragments (minimum corrected p-distance of 14.5% and 1.9% respectively) and showed consistent morphological differences (spined large styles in Part A specimens vs. smooth large styles in Part B specimens). Comparing the limited number of morphological characters against a robust and comprehensive phylogenetic (DNA) tree approved to be a fruitful approach for integrating the strengths of morphological data with those of sequence data.
Part A contains Plocamionida ambigua s.l. and the forms described by Brøndsted  as f. tornotata, f. tylotata and f. grandichelata. Specimens of ESU H5 possess the characters described by Bowerbank  for the type specimen of Plocamionida ambigua and by Brøndsted  as f. tornotata. Haplotype H6 specimens possess the characters described by Brøndsted  as f. tylotata and haplotype H4 specimens possess the characters described by Brøndsted  as f. grandichelata. Given these morphological differences and the high genetic distance between H4 and H6 specimens (corrected p-distance of 3.2% in COI and 0.7% in 28S), as well as between H4 and H5 (corrected p-distance of 2.3% in COI and 0.1% in 28S), f. tylotata and f. grandichelata can be considered valid species, whereas f. tornata corresponds to the species P. ambigua. Three Gulf of Cadiz specimens of Part A (H1–3) appear to have deviating characters from the other Plocamionida specimens (spined large styles, tylote tornotes, simple shape of the spines in the acanthostrongyle and large chelae). This observation, in addition to the presence of unique haplotypes, divergent from the most closely related species (P.tylotata, H6) by p-distance values from 1.3% to 2.4% in COI and from 0.5% to 1% in 28S suggests that these specimens may actually be undescribed Plocamionida species. However, no morphological characters could distinguish the three different specimens from each other. Evidently, a larger number of specimens from these ESUs need to be analyzed to infer whether they may form a cryptic species complex.
Part B conforms almost entirely with the description of Plocamionida microcionides (Carter, 1876) as redescribed by Stephens . Only the above mentioned H8e from the Gulf of Cadiz deviates by having large chelae, a characteristic used so far as critical to delineate species, in combination with molecular data. This one COI sequence indicates that the classification of species purely by means of morphology may be difficult and that the size of the chelae within Plocamionida species can be an ambiguous diagnostic character in some Plocamionida species. It again emphasizes the need to study morphological variation in combination with other data, such as genetic variation. In addition, H7 is highly divergent from the other P. microcionides specimens in the molecular analyses of COI and 28S (p-distance values of 1.9% and 0.1% respectively) and the combined partitions, but its morphological features are identical to the ones of Part B. This may indicate that P. microcionides is actually a species complex. However, more specimens of H7 are required to support this hypothesis. Additional investigations (behavioural, ecological, etc.) and further taxonomic analyses (cytology, chemistry) might also be needed.
The high and non-overlapping genetic divergence values among ESUs (from 1.3% to 20%), and within the more widespread and genetically diverse species H8 (0.5%, Table 1) indicates the usefulness of the COI partitions for the molecular distinction of species in our data set. A slightly lower ratio of transition/transversions (1.45 vs. 1.941) was observed in I3M11 vs. M1M6 partitions when using the 27 specimens for which both M1M6 and I3M11 sequences were available. It confirms the more progressive stage in character evolution of the I3M11 partition compared to the M1M6 partition . Moreover, the I3M11 partition was much easier to amplify than the M1M6 partition. Sequences of the M1M6 partition were more often impeded by contaminations (hydrozoans, microbial symbionts, etc.). Our study further confirms the resolution power and suitability of the I3M11 COI partition for low level phylogenies such as barcoding, (Sponge Barcoding project,), as the same number of ESU (eight) was detected using the M1M6 and I3M11 partitions separately or even jointly. Although the low COI genetic differences between some of the ESUs (Table 1:1.3 to 1.9%) are clearly smaller than the interspecific distances found within other genera, such as Hexadella (Order Verongida, 3.9 to 8.7% ) or Scopalina (Order Halichondrida, 11 to 22% ), Poppe et al.  reported very low genetic distance values (maximum 1.8%) between morphologically distinct Psammocinia species (Order Dictyoceratida). Consequently, the COI marker seems to show different levels of genetic variation between different sponge taxa. The 28S tree showed major congruences with the COI tree, although the number of highly supported clades recovered in 28S was lower. This marker, in combination with COI, was found suitable to highlight putative cryptic species within Plocamionida, such as H1–3 and H7–8. The combination between molecular data and morphological characters proved useful for differentiating Plocamionida species and for establishing their phylogenetic relationships. All trees showed the same topology, which confirms the consistency of the arrangement. This study reinforces the utility of integrative taxonomy , –.
Bathymetric and geographic distribution of Plocamionida species
P.tylotata, and P.ambigua were shown to present a wide bathymetric range distribution, with records in both deep (Skagerrak and Mingulay CWRs respectively), and shallow water (the Irish locality), while P.microcionides and P.grandichelata were found only in deeper habitats (≥50 m; , ,  this study). So far, P.grandichelata was only reported from Scandinavian waters (the Faroe, ; CWRs area from Bergen and Skagerrak, this study). Interestingly, our data suggests that the deep habitats of the Gulf of Cadiz area harbors the highest diversity, with four ESUs observed out of four samples (Fig. 1). Currently there is one described Plocamionida species from the Antarctic (Plocamionida gaussiana (Hentschel, 1914), one from Washington (USA) (Plocamionida lyoni (Bakus, 1966), one from St Georges, Grenada (Plocamionida topsenti Burton, 1954) and none of them have been reported in the NE Atlantic. In addition, P. gaussiana and P. lyoni may lack proper short echinating acanthostyles, a morphological criteria shared by P. topsenti and the European Plocamionida species. Consequently, most of the ESUs investigated here might represent new taxa and our data show that the current number of Plocamionida species of the NE Atlantic waters may be underestimated. We did not encounter any individual that could be assigned to an achelata variety Topsent, 1928, but its existence may also indicate further diversity in the genus Plocamionida. A possible radiation of Plocamionida in the Gulf of Cadiz is suggested by our data, supporting the idea that ‘low latitude’ CWRs act as diversity hot-spots. Similarly, the bathyal Gulf of Cadiz area showed particularly high species diversity of marine hydroids , while an unprecedented number of unique evolutionary lineages of tubeworms was reported from the Gulf of Cadiz mud volcanoes . Obviously, the sharp environmental discontinuities in temperature, pressure and nutrient richness (including silica concentration) in shallow water vs. deep-water coral reef habitats may have a great potential for sponge evolution. Our study adds to the growing evidence of genetically highly diverse CWRs and is expected to contribute to an improved understanding of the role of CWRs in the sustenance of sponge distributions along the coasts of Europe.
Following an “integrative taxonomy” approach to study species from multiple, complementary perspectives , this study provides evidence that P. grandichelata, P. tylotata, P. ambigua and P. microcionides in the NE Atlantic are valid species, and suggests the existence of putatively new Plocamionida species. Those hypothetical species are now submitted to the filter of other approaches and further sampling followed by detailed phenotypic diagnostic analyses may support the observed molecular differences. New species are indeed important to consider for the protection of cold-water coral reefs, which are increasingly shown as reservoirs of biodiversity. On the other hand, the unexpected high level of Plocamionida biodiversity, found in the Gulf of Cadiz especially illustrates the problem of obtaining sufficient specimens in any one deep-sea sponge species from CWRs for phylogeographic studies. The higher amplification success and higher resolution power of I3M11 adds to the growing evidence that it may be a better COI partition than M1M6 to infer inter- and intraspecific diversity.
Plocamionida specimens analysed in the present study. Information regarding the corresponding Evolutionary Significant Unit (ESU), sampling (code, localities with their abbreviation in parenthesis, sampling method, Field Number, voucher specimen, coordinates, depth), number of individuals studied (N) and number of different haplotypes (Nh) for each marker (COI M1M6 and I3M11 partition, 28S) is provided. Sampling location abbreviations are given in uppercase letters for deep-water samples (>50 m) and in lowercase letters for shallow-water samples.
Thanks are due to the captains and crew of R/V Belgica and R/V Pelagia. We are grateful to Paco Cardenas and Joana Xavier for providing useful discussions about data analyses and to Claire Goodwin for helpful remarks on the morphology of the studied material. Isabelle Domart-Coulon (Muséum National d'Histoire Naturelle, Paris) is warmly acknowledged for providing facilities at the Museum. This work benefited from the useful comments of two anonymous referees.
Conceived and designed the experiments: JR RS. Performed the experiments: JR AR RS. Analyzed the data: JR RS BP SD. Contributed reagents/materials/analysis tools: AV RS. Wrote the paper: JR RS SD.
- 1. Jensen A, Frederiksen R (1992) The Fauna associated with the bank-forming deepwater coral Lophelia pertusa (Scleractinaria) on the Faroe shelf. Sarsia 77: 53–69.A. JensenR. Frederiksen1992The Fauna associated with the bank-forming deepwater coral Lophelia pertusa (Scleractinaria) on the Faroe shelf.Sarsia775369
- 2. Rogers AD (1999) The biology of Lophelia pertusa (Linnaeus 1758) and other deep-water reef-forming corals and impacts from human activities. International Review of Hydrobiology 84: 315–406.AD Rogers1999The biology of Lophelia pertusa (Linnaeus 1758) and other deep-water reef-forming corals and impacts from human activities.International Review of Hydrobiology84315406
- 3. Van Soest RWM, Cleary DFR, de Kluijver MJ, Lavaleye MSS, Maier C, et al. (2007) Sponge diversity and community composition in Irish bathyal coral reefs. Contributions to Zoology 76: 121–142.RWM Van SoestDFR ClearyMJ de KluijverMSS LavaleyeC. Maier2007Sponge diversity and community composition in Irish bathyal coral reefs.Contributions to Zoology76121142
- 4. Barthel D (1991) Influence of different current regimes on the growth form of Halichondria panicea Pallas. In: Reitner J, Kreupp H, editors. Fossil and Recent Sponges. Berlin: Springer. pp. 387–394.D. Barthel1991Influence of different current regimes on the growth form of Halichondria panicea PallasJ. ReitnerH. KreuppFossil and Recent SpongesBerlinSpringer387394
- 5. Rice AL, Thurston MH, New AL (1990) Dense Aggregations of a Hexactinellid Sponge Pheronema carpenteri in the Porcupine Seabight (Northeast Atlantic-Ocean), and Possible Causes. Progress in Oceanography 24: 179–196.AL RiceMH ThurstonAL New1990Dense Aggregations of a Hexactinellid Sponge Pheronema carpenteri in the Porcupine Seabight (Northeast Atlantic-Ocean), and Possible Causes.Progress in Oceanography24179196
- 6. Klitgaard AB, Tendal OS (2004) Distribution and species composition of mass occurrences of large-sized sponges in the northeast Atlantic. Progress In Oceanography 61: 57–98.AB KlitgaardOS Tendal2004Distribution and species composition of mass occurrences of large-sized sponges in the northeast Atlantic.Progress In Oceanography615798
- 7. Vacelet J (1969) Éponges de la Roche du Large et de l'étage bathyal de Méditérranée (Récoltes de la soucoupe plongeante Cousteau et dragages). Mémoires du Muséum national d'Histoire naturelle (A, Zoologie) 59: 145–219, pls I-IV.J. Vacelet1969Éponges de la Roche du Large et de l'étage bathyal de Méditérranée (Récoltes de la soucoupe plongeante Cousteau et dragages).Mémoires du Muséum national d'Histoire naturelle (A, Zoologie)59145219, pls I-IV
- 8. Longo C, Mastrototaro F, Corriero G (2005) Sponge fauna associated with a Mediterranean deep-sea coral bank. Journal of the Marine Biological Association of the UK 85: 1341–1352.C. LongoF. MastrototaroG. Corriero2005Sponge fauna associated with a Mediterranean deep-sea coral bank.Journal of the Marine Biological Association of the UK8513411352
- 9. Van Soest RWM, Lavaleye MSS (2005) Diversity and abundance of sponges in bathyal coral reefs of Rockall Bank, NE Atlantic, from boxcore samples. Marine Biology Research: 1: 338–349.RWM Van SoestMSS Lavaleye2005Diversity and abundance of sponges in bathyal coral reefs of Rockall Bank, NE Atlantic, from boxcore samples.Marine Biology Research:1338349
- 10. Reveillaud J, Remerie T, van Soest R, Erpenbeck D, Cárdenas P, et al. (2010) Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae). Molecular Phylogenetics and Evolution 56: 104–114.J. ReveillaudT. RemerieR. van SoestD. ErpenbeckP. Cárdenas2010Species boundaries and phylogenetic relationships between Atlanto-Mediterranean shallow-water and deep-sea coral associated Hexadella species (Porifera, Ianthellidae).Molecular Phylogenetics and Evolution56104114
- 11. Roberts JM, Wheeler AJ, Freiwald A (2006) Reefs of the deep: The biology and geology of cold-water coral ecosystems. Science 312: 543–547.JM RobertsAJ WheelerA. Freiwald2006Reefs of the deep: The biology and geology of cold-water coral ecosystems.Science312543547
- 12. Faulkner DJ (2000) Highlights of marine natural products chemistry (1972–1999). Natural Product Report 17: 1–6.DJ Faulkner2000Highlights of marine natural products chemistry (1972–1999).Natural Product Report1716
- 13. Boury-Esnault N, Pansini M, Uriz MJ (1994) Spongiaires bathyaux de la mer d'Alboran et du golfe ibéro-marocain. Mémoires du Muséum national d'Histoire naturelle 160: 1–174.N. Boury-EsnaultM. PansiniMJ Uriz1994Spongiaires bathyaux de la mer d'Alboran et du golfe ibéro-marocain.Mémoires du Muséum national d'Histoire naturelle1601174
- 14. Stephens J (1921) Sponges of the coast of Ireland. II.-The Tetraxonida (Concluded). Fisheries Ireland: Sci. Investigations. pp. 1–75.J. Stephens1921Sponges of the coast of Ireland. II.-The Tetraxonida (Concluded).Fisheries IrelandSci. Investigations175
- 15. Topsent E (1928) Spongiaires de l'Atlantique et de la Méditerranée provenant des croisières du Prince Albert ler de Monaco. Résultats des campagnes scientifiques accomplies par le Prince Albert I Monaco 74: 1–376, pls I-XI.E. Topsent1928Spongiaires de l'Atlantique et de la Méditerranée provenant des croisières du Prince Albert ler de Monaco.Résultats des campagnes scientifiques accomplies par le Prince Albert I Monaco741376, pls I-XI
- 16. Alander H (1942) Sponges from the Swedish West-Coast and adjacent waters. Ph.D. Thesis. (University of Lund, H. Struves: Gøteborg). pp. 1–95, 15 pls.H. Alander1942Sponges from the Swedish West-Coast and adjacent waters.Ph.D. Thesis. (University of Lund, H. Struves: Gøteborg)195, 15 pls
- 17. Picton BE, Goodwin CE (2007) Sponge biodiversity of Rathlin Island, Northern Ireland. Journal of the Marine Biological Association of the United Kingdom 87: 1441–1458.BE PictonCE Goodwin2007Sponge biodiversity of Rathlin Island, Northern Ireland.Journal of the Marine Biological Association of the United Kingdom8714411458
- 18. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R (1994) DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294–299.O. FolmerM. BlackW. HoehR. LutzR. Vrijenhoek1994DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.Molecular Marine Biology and Biotechnology3294299
- 19. Shearer TL, van Oppen MJH, Romano SL, Worheide G (2002) Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Molecular Ecology 11: 2475–2487.TL ShearerMJH van OppenSL RomanoG. Worheide2002Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria).Molecular Ecology1124752487
- 20. Wörheide G (2006) Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific. Marine Biology 148: 907–912.G. Wörheide2006Low variation in partial cytochrome oxidase subunit I (COI) mitochondrial sequences in the coralline demosponge Astrosclera willeyana across the Indo-Pacific.Marine Biology148907912
- 21. Duran S, Pascual M, Turon X (2004) Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge Crambe crambe (Poecilosclerida). Marine Biology 144: 31–35.S. DuranM. PascualX. Turon2004Low levels of genetic variation in mtDNA sequences over the western Mediterranean and Atlantic range of the sponge Crambe crambe (Poecilosclerida).Marine Biology1443135
- 22. Erpenbeck D, Breeuwer J, van der Velde H, van Soest RWM (2002) Unravelling host and symbiont phylogenies of halichondrid sponges (Demospongiae, Porifera) using a mitochondrial marker. Marine Biology 141: 377–386.D. ErpenbeckJ. BreeuwerH. van der VeldeRWM van Soest2002Unravelling host and symbiont phylogenies of halichondrid sponges (Demospongiae, Porifera) using a mitochondrial marker.Marine Biology141377386
- 23. Duran S, Rutzler K (2006) Ecological speciation in a Caribbean marine sponge. Molecular Phylogenetics and Evolution 40: 292–297.S. DuranK. Rutzler2006Ecological speciation in a Caribbean marine sponge.Molecular Phylogenetics and Evolution40292297
- 24. Wulff JL (2006) Sponge Systematics by Starfish: Predators Distinguish Cryptic Sympatric Species of Caribbean Fire Sponges, Tedania ignis and Tedania klausi n. sp. (Demospongiae, Poecilosclerida). Biological Bulletin 211: 83–94.JL Wulff2006Sponge Systematics by Starfish: Predators Distinguish Cryptic Sympatric Species of Caribbean Fire Sponges, Tedania ignis and Tedania klausi n. sp. (Demospongiae, Poecilosclerida).Biological Bulletin2118394
- 25. Blanquer A, Uriz MJ (2007) Cryptic speciation in marine sponges evidenced by mitochondrial and nuclear genes: A phylogenetic approach. Molecular Phylogenetics and Evolution 45: 392–397.A. BlanquerMJ Uriz2007Cryptic speciation in marine sponges evidenced by mitochondrial and nuclear genes: A phylogenetic approach.Molecular Phylogenetics and Evolution45392397
- 26. Erpenbeck D, Hooper JNA, Worheide G (2006) CO1 phylogenies in diploblasts and the ‘Barcoding of Life’ - are we sequencing a suboptimal partition? Molecular Ecology Notes 6: 550–553.D. ErpenbeckJNA HooperG. Worheide2006CO1 phylogenies in diploblasts and the ‘Barcoding of Life’ - are we sequencing a suboptimal partition?Molecular Ecology Notes6550553
- 27. Xavier JR, Rachello-Dolmen PG, Parra-Velandia F, Schönberg CHL, Breeuwer JAJ, et al. (2010) Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae). Molecular Phylogenetics and Evolution 56: 13–20.JR XavierPG Rachello-DolmenF. Parra-VelandiaCHL SchönbergJAJ Breeuwer2010Molecular evidence of cryptic speciation in the “cosmopolitan” excavating sponge Cliona celata (Porifera, Clionaidae).Molecular Phylogenetics and Evolution561320
- 28. Lopez-Legentil S, Pawlik JR (2009) Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI. Coral Reefs 28: 157–165.S. Lopez-LegentilJR Pawlik2009Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI.Coral Reefs28157165
- 29. Xavier JR, van Soest RWM, Breeuwer JAJ, Martins AMF, Menken SBJ (2010) Phylogeography, genetic diversity and structure of the poecilosclerid sponge Phorbas fictitius at oceanic islands. Contributions to Zoology 79: 119–129.JR XavierRWM van SoestJAJ BreeuwerAMF MartinsSBJ Menken2010Phylogeography, genetic diversity and structure of the poecilosclerid sponge Phorbas fictitius at oceanic islands.Contributions to Zoology79119129
- 30. Lindner A, Cairns SD, Cunningham CW (2008) From Offshore to Onshore: Multiple Origins of Shallow-Water Corals from Deep-Sea Ancestors. Plos One 3: e2429.A. LindnerSD CairnsCW Cunningham2008From Offshore to Onshore: Multiple Origins of Shallow-Water Corals from Deep-Sea Ancestors.Plos One3e2429
- 31. Rot C, Goldfarb I, Ilan M, Huchon D (2006) Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria. BMC Evolutionary Biology 71.C. RotI. GoldfarbM. IlanD. Huchon2006Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria.BMC Evolutionary Biology71
- 32. McCormack GP, Kelly M (2002) New indications of the phylogenetic affinity of Spongosorites suberitoides Diaz et al., 1993 (Porifera, Demospongiae) as revealed by 28S ribosomal DNA. J Nat Hist 36: 1009–1021.GP McCormackM. Kelly2002New indications of the phylogenetic affinity of Spongosorites suberitoides Diaz et al., 1993 (Porifera, Demospongiae) as revealed by 28S ribosomal DNA.J Nat Hist3610091021
- 33. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059–3066.K. KatohK. MisawaK. KumaT. Miyata2002MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.Nucleic Acids Research3030593066
- 34. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods), ver. 4.0. beta 10. Sunderland, MA: Sinauer Associates. DL Swofford2002PAUP*. Phylogenetic Analysis Using Parsimony (* and other methods), ver. 4.0. beta 10.Sunderland, MASinauer Associates
- 35. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.F. RonquistJP Huelsenbeck2003MrBayes 3: Bayesian phylogenetic inference under mixed models.Bioinformatics1915721574
- 36. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817–818.D. PosadaKA Crandall1998Modeltest: testing the model of DNA substitution.Bioinformatics14817818
- 37. Nylander JAA (2002) JAA Nylander2002MrModeltest v.1.0. Program distributed by the author. Department of Systematic Zoology, Uppsala University, Uppsala. [http://www.ebc.uu.se/systzoo/staff/nylander.html]. MrModeltest v.1.0. Program distributed by the author. Department of Systematic Zoology, Uppsala University, Uppsala. [http://www.ebc.uu.se/systzoo/staff/nylander.html].
- 38. Brøndsted HV (1932) Marine Spongia. The Zoology of the Faroes 1: 1–34.HV Brøndsted1932Marine Spongia.The Zoology of the Faroes1134
- 39. Bowerbank JS (1866) A Monograph of the British Spongiadæ Volume 2: London: Ray Society. i-xx, 1–388 p.JS Bowerbank1866A Monograph of the British SpongiadæVolume 2LondonRay Societyi-xx, 1388 p
- 40. Poppe J, Sutcliffe P, Hooper JNA, Worheide G, Erpenbeck D (2010) CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida). Plos One. 5. e9950 p.J. PoppeP. SutcliffeJNA HooperG. WorheideD. Erpenbeck2010CO I Barcoding Reveals New Clades and Radiation Patterns of Indo-Pacific Sponges of the Family Irciniidae (Demospongiae: Dictyoceratida).Plos One5e9950
- 41. Dayrat B (2005) Towards integrative taxonomy. Biological Journal of the Linnean Society 85: 407–415.B. Dayrat2005Towards integrative taxonomy.Biological Journal of the Linnean Society85407415
- 42. Wahlberg N, Braby MF, Brower AVZ, de Jong R, Lee MM, et al. (2005) Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers. Proceedings of the Royal Society B-Biological Sciences 272: 1577–1586.N. WahlbergMF BrabyAVZ BrowerR. de JongMM Lee2005Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers.Proceedings of the Royal Society B-Biological Sciences27215771586
- 43. Fonseca G, Derycke S, Moens T (2008) Integrative taxonomy in two free-living nematode species complexes. Biological Journal of the Linnean Society 94: 737–753.G. FonsecaS. DeryckeT. Moens2008Integrative taxonomy in two free-living nematode species complexes.Biological Journal of the Linnean Society94737753
- 44. Carter HJ (1876) Descriptions and Figures of Deep-Sea Sponges and their Spicules, from the Atlantic Ocean, dredged up on board H.M.S. ‘Porcupine’, chiefly in 1869 (concluded). Annals and Magazine of Natural History 4: 226–240;.HJ Carter1876Descriptions and Figures of Deep-Sea Sponges and their Spicules, from the Atlantic Ocean, dredged up on board H.M.S. ‘Porcupine’, chiefly in 1869 (concluded).Annals and Magazine of Natural History4226240;307-324;. 388-410;. 458-479, pls XII-XVI. 458-479, pls XII-XVI.
- 45. Moura CJ, Harris DJ, Cunha MR, Rogers AD (2008) DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments. Zoologica Scripta 37: 93–108.CJ MouraDJ HarrisMR CunhaAD Rogers2008DNA barcoding reveals cryptic diversity in marine hydroids (Cnidaria, Hydrozoa) from coastal and deep-sea environments.Zoologica Scripta3793108
- 46. Hilario A, Johnson SB, Cunha MR, Vrijenhoek RC (2010) High diversity of frenulates (Polychaeta: Siboglinidae) in the Gulf of Cadiz mud volcanoes: A DNA taxonomy analysis. Deep-Sea Research Part I-Oceanographic Research Papers 57: 143–150.A. HilarioSB JohnsonMR CunhaRC Vrijenhoek2010High diversity of frenulates (Polychaeta: Siboglinidae) in the Gulf of Cadiz mud volcanoes: A DNA taxonomy analysis.Deep-Sea Research Part I-Oceanographic Research Papers57143150