Novel microsatellite markers suggest significant genetic isolation in the Eastern Pacific sponge Aplysina gerardogreeni.

BACKGROUND: The Eastern Tropical Pacific (ETP) harbors a great diversity of Porifera. In particular, the Aplysina genus has acquired biotechnological and pharmacological importance. Nevertheless, the ecological aspects of their species and populations have been poorly studied. Aplysina gerardogreeni is the most conspicuous verongid sponge from the ETP, where it is usually found on rocky-coralline ecosystems. We evaluated the polymorphism levels of 18 microsatellites obtained from next-generation sequencing technologies. Furthermore, we tested the null hypothesis of panmixia in A. gerardogreeni population from two Mexican-Pacific localities. METHODS AND RESULTS: A total of 6,128,000 paired reads were processed of which primer sets of 18 microsatellites were designed. The loci were tested in 64 specimens from Mazatlan, Sinaloa (N = 32) and Isabel Island, Nayarit (N = 32). The microsatellites developed were moderately polymorphic with a range of alleles between 2 and 11, and Ho between 0.069 and 0.785. Fifteen loci displayed significant deviation from the Hardy-Weinberg equilibrium. No linkage disequilibrium was detected. A strong genetic structure was confirmed between localities using hierarchical Bayesian analyses, principal coordinates analyses, and fixation indices (FST = 0.108*). All the samples were assigned to their locality; however, there was a small sign of mixing between localities. CONCLUSIONS: Despite the moderate values of diversity in microsatellites, they showed a strong signal of genetic structure between populations. We suggest that these molecular markers can be a relevant tool to evaluate all populations across the ETP. In addition, 17 of these microsatellites were successfully amplified in the species A. fistularis and A. lacunosa, meaning they could also be applied in congeneric sponges from the Caribbean Sea. The use of these molecular markers in population genetic studies will allow assessment of the connectivity patterns in species of the Aplysina genus.

Isolation and characterization of novel microsatellite loci for the Eastern Pacific marine sponge Mycale cecilia by Illumina MiSeq sequencing.

BACKGROUND: Mycale cecilia is an abundant Eastern Tropical Pacific sponge living in a wide variety of habitats, including coral reefs where it may directly interact with corals. It is also known to possess secondary metabolites of pharmacological value. These aspects highlight the importance of having a better understanding of its biology, and genetic and population diversity. METHODS AND RESULTS: In the present study, we isolated and characterized twelve novel microsatellite loci by Illumina MiSeq sequencing. The loci were tested in 30 specimens collected from two coral reef localities (La Paz, Baja California Sur and Isabel Island, Nayarit) from the Mexican Pacific using M13(-21) labeling. All loci were polymorphic, with two to nine alleles per locus. Expected heterozygosities varied from 0.616 to 0.901. Eleven loci were tested and successfully amplified in M. microsigmatosa from the Gulf of Mexico. CONCLUSION: Here we report the first microsatellite loci developed for a sponge species from the Eastern Pacific coast. These molecular markers will be used for population genetic studies of M. cecilia, and potentially in other congeneric species; particularly in vulnerable marine areas that require protection, such as coral reefs.

Redescription of Lernaeenicus longiventris Wilson, 1917 (Copepoda: Pennellidae) Parasitic on the Pacific Crevalle Jack Caranx caninus (Carangidae) Through Morphological and Molecular Analyses.

PURPOSE: The present study deals with a redescription of the copepod Lernaeenicus longiventris Wilson, 1917 (Copepoda: Siphonostomatoida: Pennellidae) found on the Pacific crevalle jack Caranx caninus Günther, using morphological and molecular analyses. METHODS: Fish were collected off Mazatlán Port (23° 12' N, 106° 26' W), in the State of Sinaloa, Mexico (southeastern Gulf of California). The copepods were morphologically analyzed by light microscopy. Sequences of the COI mtDNA gene were generated for the first time for this species. These sequences were compared to COI sequences from six species of Lernaeenicus available in GenBank. RESULTS: The specimens of the present study exhibited a cephalosome without apparent lateral processes, which were originally described for L. longiventris. No remarkable differences were observed with previous descriptions regarding appendages and body proportions. The phylogenetic tree based on COI sequences showed that L. longiventris was closer to L. radiatus although with low bootstrap values support in ML tree, both species formed a sister clade of L. sprattae. CONCLUSIONS: Lernaeenicus longiventris is the unique species of the genus in the Mexican Pacific and the Gulf of California, and also the unique species of Lernaeenicus infecting C. caninus. Molecular data of L. longiventris from host and locality type are required to avoid misidentification of this species.

De novo transcriptome assembly for two color types of the marine sponge Mycale (Carmia) cecilia.

Despite the ecological importance and the potential pharmacological application of the sponge Mycale (Carmia) cecilia, it is uncertain whether the body-color variation, even in individuals coexisting in the same area, is due to intraspecific phenotypic plasticity or corresponds to taxonomic divergence. This uncertainty is relatively common in several Porifera groups, which lack the resolution of morphological diagnostic characters and slow-evolving mitochondrial genomes as occurs in early splitting lineages. We sequenced the RNA of six individuals with two different body-color (green-morphotype and red-morphotype) collected at the same time side by side. High-throughput sequencing of cDNA libraries produced ~ 129 million reads with a length of 150 bp. Each morphotype was assembled separately owing to the low overlapping in the global assembly. Metatranscriptome de novo assembly of the trimmed and normalized reads produced 461 thousand transcripts for the green-morphotype and 342 thousand for the red-morphotype (respectively). Over 30% of the transcripts contained Open Reading Frames (ORFs) with functional significance. BUSCO analysis of the ORFs of putative poriferan origin (31.3% green or 30.4% red) indicated that our assemblies are 60% complete. This is the first attempt to evaluate the morphological diversity in the species M. (C.) cecilia and the phylum Porifera at the transcriptomic level. Due to the minimum overlap of the assembly and that, the red-morphotype diverged significantly from the green-morphotype (original color of M. (C.) cecilia). Therefore, we suggest that the red-morphotype should undergo a complete taxonomic investigation and its taxonomic status be reviewed. We expect that the transcriptome assembly metrics can be useful for comparing other transcriptome assemblies of non-model organisms.

Sponge diversity in Eastern Tropical Pacific coral reefs: an interoceanic comparison.

Sponges are an important component of coral reef communities. The present study is the first devoted exclusively to coral reef sponges from Eastern Tropical Pacific (ETP). Eighty-seven species were found, with assemblages dominated by very small cryptic patches and boring sponges such as Cliona vermifera; the most common species in ETP reefs. We compared the sponge patterns from ETP reefs, Caribbean reefs (CR) and West Pacific reefs (WPR), and all have in common that very few species dominate the sponge assemblages. However, they are massive or large sun exposed sponges in CR and WPR, and small encrusting and boring cryptic species in ETP. At a similar depth, CR and WPR had seven times more individuals per m2, and between four (CR) and five times (WPR) more species per m2 than ETP. Perturbation, at local and large scale, rather than biological factors, seems to explain the low prevalence and characteristics of sponge assemblages in ETP reefs, which are very frequently located in shallow water where excessive turbulence, abrasion and high levels of damaging light occur. Other factors such as the recurrence of large-scale phenomena (mainly El Niño events), age of the reef (younger in ETP), isolation (higher in ETP), difficulty to gain recruits from distant areas (higher in ETP), are responsible for shaping ETP sponge communities. Such great differences in sponge fauna between the three basins might have consequences for coral reef structure and dynamics.

The complete mitogenome of the Eastern Pacific sponge Aplysina gerardogreeni (Demospongiae, Verongida, Aplysinidae).

We report the first mitochondrial genome of a Verongid sponge, Aplysina gerardogreeni from the Pacific Ocean. This has 19,620 bp and includes 14 protein-coding genes, 2 rRNAs genes, and 25 tRNAs genes. The gene arrangement was similar to the one found in two Caribbean Aplysina mitogenomes previously reported. Comparative analyses revealed a few substitutions among congeneric mitogenomes. The mitogenome of A. gerardogreeni could be useful to study the evolution of Verongimorpha group and also to identify adequate genes for its molecular systematics.

Description and molecular phylogeny of Axinella nayaritensis n. sp. (Porifera: Axinellida) from East Pacific and remarks about the polyphyly of the genus Axinella.

Axinella nayaritensis n. sp. is a typical species of the genus Axinella in spiculation (oxeas and styles), skeletal arrangement (axial condensation from which radiate an extra-axial plumoreticulated skeleton), and external form (arborescent). The new species is orange, branching, up to 25 cm in height, and which usually live in soft bottoms. One of the most conspicuous characteristic of the new species is its aquiferous system, which is formed by a system of superficial canals and meandering ridges which run around the entire length of the branches. The species is compared with Axinella polycapella from Gulf of Mexico, which is very close in morphology, and which it shares a high similarity in the 18S ribosomal RNA region. It was also compared with Axinella aruensis, a very different species from a morphological point of view, which is distributed throughout the northern Australia, Indonesia and Papua New Guinea as both species share a high similarity in the COI mitochondrial gene region. The new species was included in the clade named Axinella by Gazave et al. (2010) for 18S and COI, where also are included eight Axinella-species. Species in this clade are typically arborescent with a choanosomal skeleton differentiated between axial and extra-axial regions. Axinella nayaritensis n. sp. constitute the first record of an Axinella for the east Pacific coast.

Integrative taxonomy reveals the first record and a new species for the previously monotypic genus Tethytimea (Tethyida: Tethyidae) in the Gulf of Mexico.

The first record of the previous monotypic genus Tethytimea and the description of a new species from cryptic habitats of Gulf of Mexico are presented. Tethytimea carmelita sp. nov., is a red orange cushion shaped sponge (about 5 mm thick) with a tuberculate to granular surface. The spicular complement is formed by tylostyles (200-1120 µm length), smooth spheres (12.5-55 µm in diameter); megasters-spheroxyasters (12.5-90 µm in diameter); and micrasters in two categories: oxy-strongylasters (12.5-27.5 µm in diameter) and spherotylasters (2.5-25 µm in diameter). The new species differs from the only species known T. tylota (Hentschel, 1912) mainly by differences in the size and shape of spicules. T. tylota possesses tylostyles in two size categories; megasters include giant oxyspherasters up 250 µm and micrasters in a single category. Additionally, to the morphological characteristics, we integrated partial sequences of a large sub-unit ribosomal 28S rDNA gene region (D1-D2 domains), in order to establish the molecular taxonomic position of our new species (and genus). Tree topologies (Maximum Likelihood and Bayesian Inference) were congruent in phylogenetic hypothesis, retrieving the Order Tethyida as monophyletic. In this clade, the family Timeidae was separated from the other families Tethyidae + Hemiastrellidae. Inside this latter group and according to the taxonomic hypothesis based on morphology, Tethytimea carmelita sp. nov. was included in Tethyidae clade, together with a sequence of Tethya sp. (AY626300), forming a sister group with representatives of genera Xenospongia and Thectitethya. Our new species constitutes the second valid known species for the genus Tethytimea and the first record of genus for the Atlantic Ocean.

Restriction of sponges to an atoll lagoon as a result of reduced environmental quality.

The lagoon at Palmyra Atoll in the central Pacific was subject to major military modifications during WWII and now the dominant fauna on the lagoon's hard substrate are sponges, not corals. In this study, we quantified the physical and biological factors explaining the variation in sponge distribution patterns across 11 sites to determine the potential for the sponges in the lagoon at Palmyra to invade the surrounding reef systems. Significant differences in sponge assemblages were found among all but three sites. For all the models we examined the strongest environmental relationships were found for variables related to sedimentation/turbidity and food/habitat availability. Our findings suggest that the sponges in Palmyra's lagoon are likely to be restricted to this habitat type where they are associated with conditions resulting from the earlier heavy disturbance and are unlikely to spread to the outer reef environments unless there is a dramatic decline in environmental quality.

Integrative taxonomy and molecular phylogeny of genus Aplysina (Demospongiae: Verongida) from Mexican Pacific.

Integrative taxonomy provides a major approximation to species delimitation based on integration of different perspectives (e.g. morphology, biochemistry and DNA sequences). The aim of this study was to assess the relationships and boundaries among Eastern Pacific Aplysina species using morphological, biochemical and molecular data. For this, a collection of sponges of the genus Aplysina from the Mexican Pacific was studied on the basis of their morphological, chemical (chitin composition), and molecular markers (mitochondrial COI and nuclear ribosomal rDNA: ITS1-5.8-ITS2). Three morphological species were identified, two of which are new to science. A. clathrata sp. nov. is a yellow to yellow-reddish or -brownish sponge, characterized by external clathrate-like morphology; A. revillagigedi sp. nov. is a lemon yellow to green, cushion-shaped sometimes lobate sponge, characterized by conspicuous oscules, which are slightly elevated and usually linearly distributed on rims; and A. gerardogreeni a known species distributed along the Mexican Pacific coast. Chitin was identified as the main structural component within skeletons of the three species using FTIR, confirming that it is shared among Verongida sponges. Morphological differences were confirmed by DNA sequences from nuclear ITS1-5.8-ITS2. Mitochondrial COI sequences showed extremely low but diagnostic variability for Aplysina revillagigedi sp. nov., thus our results corroborate that COI has limited power for DNA-barcoding of sponges and should be complemented with other markers (e.g. rDNA). Phylogenetic analyses of Aplysina sequences from the Eastern Pacific and Caribbean, resolved two allopatric and reciprocally monophyletic groups for each region. Eastern Pacific species were grouped in general accordance with the taxonomic hypothesis based on morphological characters. An identification key of Eastern Pacific Aplysina species is presented. Our results constitute one of the first approximations to integrative taxonomy, phylogeny and evolutionary biogeography of Eastern Pacific marine sponges; an approach that will significantly contribute to our better understanding of their diversity and evolutionary history.