The most diverse and species-rich class of the phylum Porifera is Demospongiae. In recent years, the systematics of this clade, which contains more than 7000 species, has developed rapidly in light of new studies combining molecular and morphological observations. We add more than 500 new, nearly complete 18S sequences (an increase of more than 200%) in an attempt to further enhance understanding of the phylogeny of Demospongiae. Our study specifically targets representation of type species and genera that have never been sampled for any molecular data in an effort to accelerate progress in classifying this diverse lineage. Our analyses recover four highly supported subclasses of Demospongiae: Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha. Within Keratosa, neither Dendroceratida, nor its two families, Darwinellidae and Dictyodendrillidae, are monophyletic and Dictyoceratida is divided into two lineages, one predominantly composed of Dysideidae and the second containing the remaining families (Irciniidae, Spongiidae, Thorectidae, and Verticillitidae). Within Myxospongiae, we find Chondrosida to be paraphyletic with respect to the Verongida. We amend the latter to include species of the genus Chondrosia and erect a new order Chondrillida to contain remaining taxa from Chondrosida, which we now discard. Even with increased taxon sampling of Haploscleromorpha, our analyses are consistent with previous studies; however, Haliclona species are interspersed in even more clades. Haploscleromorpha contains five highly supported clades, each more diverse than previously recognized, and current families are mostly polyphyletic. In addition, we reassign Janulum spinispiculum to Haploscleromorpha and resurrect Reniera filholi as Janulum filholi comb. nov. Within the large clade Heteroscleromorpha, we confirmed 12 recently identified clades based on alternative data, as well as a sister-group relationship between the freshwater Spongillida and the family Vetulinidae. We transfer Stylissa flabelliformis to the genus Scopalina within the family Scopalinidae, which is of uncertain position. Our analyses uncover a large, strongly supported clade containing all heteroscleromorphs other than Spongillida, Vetulinidae, and Scopalinidae. Within this clade, there is a major division separating Axinellidae, Biemnida, Tetractinellida, Bubaridae, Stelligeridae, Raspailiidae, and some species of Petromica, Topsentia, and Axinyssa from Agelasida, Polymastiidae, Placospongiidae, Clionaidae, Spirastrellidae, Tethyidae, Poecilosclerida, Halichondriidae, Suberitidae, and Trachycladus. Among numerous results: (1) Spirophorina and its family Tetillidae are paraphyletic with respect to a strongly supported Astrophorina within Tetractinellida; (2) Agelasida is the earliest diverging lineage within the second clade listed above; and (3) Merlia and Desmacella appear to be the earliest diverging lineages of Poecilosclerida.

Surprisingly, a high frequency of interspecific sea turtle hybrids has been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as Eretmochelys imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, because most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analysed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (E. imbricata), loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years.

The loggerhead sea turtle, Caretta caretta, is the most common species of sea turtle nesting in Brazil and is listed as endangered by the IUCN. Our study characterizes the genetic structure of loggerheads in Brazil based on mitochondrial DNA control region variability and presents a hypothesis for the colonization of Brazilian rookeries. We analyzed 329 samples from Brazilian rookeries and an oceanic foraging ground, and we compared our results with previously published data for other loggerhead populations. Brazilian rookeries had four haplotypes, none of which have been reported for rookeries outside Brazil. Six haplotypes were found in the foraging aggregation. The presence of the CC-A4 haplotype at all sampled sites and the low nucleotide diversity suggest a common origin for all rookeries, with CC-A4 being the ancestral haplotype of the Brazilian populations. The occurrence of three haplotypes in the foraging aggregation that are known only from rookeries outside of Brazil is consistent with the transoceanic migratory behavior of loggerheads. Our results indicated that the colonization of Brazilian rookeries probably occurred from the southern USA stock. This recent colonization most likely followed a north to south route along the Brazilian coastline, influenced by the Brazilian warm current. Our results further suggest the existence of two genetic population units of loggerheads in Brazil and corroborate natal homing behavior in loggerheads.

The endemic marine sponge Arenosclera brasiliensis (Porifera, Demospongiae, Haplosclerida) is a known source of secondary metabolites such as arenosclerins A-C. In the present study, we established the composition of the A. brasiliensis microbiome and the metabolic pathways associated with this community. We used 454 shotgun pyrosequencing to generate approximately 640,000 high-quality sponge-derived sequences (∼150 Mb). Clustering analysis including sponge, seawater and twenty-three other metagenomes derived from marine animal microbiomes shows that A. brasiliensis contains a specific microbiome. Fourteen bacterial phyla (including Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Cloroflexi) were consistently found in the A. brasiliensis metagenomes. The A. brasiliensis microbiome is enriched for Betaproteobacteria (e.g., Burkholderia) and Gammaproteobacteria (e.g., Pseudomonas and Alteromonas) compared with the surrounding planktonic microbial communities. Functional analysis based on Rapid Annotation using Subsystem Technology (RAST) indicated that the A. brasiliensis microbiome is enriched for sequences associated with membrane transport and one-carbon metabolism. In addition, there was an overrepresentation of sequences associated with aerobic and anaerobic metabolism as well as the synthesis and degradation of secondary metabolites. This study represents the first analysis of sponge-associated microbial communities via shotgun pyrosequencing, a strategy commonly applied in similar analyses in other marine invertebrate hosts, such as corals and algae. We demonstrate that A. brasiliensis has a unique microbiome that is distinct from that of the surrounding planktonic microbes and from other marine organisms, indicating a species-specific microbiome.

BackgroundDemosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges.Methodology/Principal FindingsWe generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida.Conclusions/SignificanceThese results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

A great number of marine organisms lack proper morphologic characters for identification and species description. This could promote a wide distributional pattern for a species morphotype, potentially generating many morphologically similar albeit evolutionarily independent worldwide lineages. This work aimed to estimate the genetic variation of South America populations of the Cliona celata species complex. We used COI mtDNA and ITS rDNA as molecular markers and tylostyle length and width as morphological characters to try to distinguish among species. Four distinct clades were found within the South American C. celata complex using both genetic markers. The genetic distances comparisons revealed that scores among those clades were comparable to distances between each clade and series of previously described clionaid species, some of which belong to different genera. Our results also suggest that one of the clades has a broad discontinuous distribution in the Atlantic Ocean, while another presents high gene flow between the southern Atlantic and Pacific coasts of South America. Conversely, spicule morphology was not able to distinguish each clade, due to the high degree of overlap among them. Therefore, we considered that each recovered clade correspond, in fact, to different species that cannot be differentiated via morphological characters, which are often used to describe species within the C. celata species complex.

The coastline of Sergipe state hosts the main Brazilian nesting sites of Lepidochelys olivacea (Eschscholtz, 1829). The second most abundant species of turtles in Sergipe is Caretta caretta (Linnaeus, 1758). Both sea turtle species, respectively known as olive ridley and loggerhead, are currently listed as endangered by the International Union for the Conservation of Nature and Natural Resources. The genetic diversity of the Sergipe loggerhead population (N = 51) was assayed by analyzing 627 bp from the control region of mitochondrial DNA in nesting females. Three haplotypes were identified: CC-A4, CC-A24 and CC 9 LO. The last one was recorded for specimens considered hybrids because they represent L. olivacea's mtDNA, but had the external morphology of C. caretta or of a mixture of both species. Based on the two types of hybrids, it was hypothesized that at least two hybridization events had occurred: a more ancient hybridization event, accompanied by introgression (F2 or later backcrosses), and a recent one (F1), both of which involving the same L. olivacea haplotype. The incidence of L. olivacea mitochondrial genome introgression into the C. caretta rookeries was only observed in Sergipe, which could be related to the large numbers of L. olivacea in this region and an overlap of reproduction periods and distribution areas of both species. This may also be associated to global warming since it might alter the sex ratio of sea turtles, thus facilitating interspecific mating. Awareness of gene flow between these species will significantly influence the development and implementation of adequate management strategies.

This article reports on 12 new species originating from the Chilean fjords region, namely Clathria (Microciona) mytilifila sp. nov., Haliclona (Reniera) caduca sp. nov., Latrunculia (L.) ciruela sp. nov., Latrunculia (L.) copihuensis sp. nov., Latrunculia (L.) verenae sp. nov., Latrunculia (L.) yepayek sp. nov., Myxilla (Burtonanchora) araucana sp. nov., Neopodospongia tupecomareni sp. nov., Oceanapia guaiteca sp. nov., Oceanapia spinisphaera sp. nov., Suberites cranium sp. nov. and Tethya melinka sp. nov. The material studied was collected between 5 and 30 m depth at latitudes comprised between 42º and 50ºS, and is part of a large collection of Chilean sponges gathered by an international team in a series of expeditions. Identification keys are provided for SE Pacific Suberites and Latrunculia, and the known species of Myxilla (Burtonanchora) and Neopodospongia. A trans-Pacific link to the New Zealand fauna was retrieved for the latter genus. Distribution ranges apparent from the materials studied here are judged too preliminary to allow any inference on biotic boundaries in the SE Pacific. A revision of earlier assertions about these biogeographic units and their boundaries concluded that very little support remains other than for existence of a Magellanic fauna. This is in part a consequence of revising the taxonomy of sponge species originally deemed to underpin these areas. Specifically, the former proposal of a Central to Southern Chile biogeographic unit (33-56ºS) has been markedly undone.