An analysis of partial 28S ribosomal RNA sequences suggests early radiations of sponges

Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of Heteroscleromorpha (Porifera: Demospongiae)

Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly challenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Lévi, 1953. Axinellida occupies a key position in different morphologically derived topologies. The abandonment of Axinellida and the establishment of Halichondrida Vosmaer, 1887 sensu lato to contain Halichondriidae Gray, 1867, Axinellidae Carter, 1875, Bubaridae Topsent, 1894, Heteroxyidae Dendy, 1905, and a new family Dictyonellidae van Soest et al., 1990 was based on the conclusion that an axially condensed skeleton evolved independently in separate lineages in preference to the less parsimonious assumption that asters (star-shaped spicules), acanthostyles (club-shaped spicules with spines), and sigmata (C-shaped spicules) each evolved more than once. Our new molecular trees are congruent and contrast with the earlier, morphologically based, trees. The results show that axially condensed skeletons, asters, acanthostyles, and sigmata are all homoplasious characters. The unrecognized homoplasious nature of these characters explains much of the incongruence between molecular-based and morphology-based phylogenies. We use the molecular trees presented here as a basis for re-interpreting the morphological characters within Heteroscleromorpha. The implications for the classification of Heteroscleromorpha are discussed and a new order Biemnida ord. nov. is erected.

Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes

BACKGROUND

Demosponges 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 FINDINGS

We 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: Keratosa(p), Myxospongiae(p), Spongillida(p), Haploscleromorpha(p) (the marine haplosclerids) and Democlavia(p). We found conflicting results concerning the relationships of Keratosa(p) and Myxospongiae(p) to the remaining demosponges, but our results strongly supported a clade of Haploscleromorpha(p)+Spongillida(p)+Democlavia(p). In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillida(p)) are sister to Haploscleromorpha(p) rather than part of Democlavia(p). Within Keratosa(p), we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiae(p), Chondrosida and Verongida were monophyletic. A well-supported clade within Democlavia(p), Tetractinellida(p), 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 Democlavia(p). Within Tetractinellida(p), 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/SIGNIFICANCE

These 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.

Sponge systematics facing new challenges

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.

Deep phylogeny and evolution of sponges (phylum Porifera)

Sponges (phylum Porifera) are a diverse taxon of benthic aquatic animals of great ecological, commercial, and biopharmaceutical importance. They are arguably the earliest-branching metazoan taxon, and therefore, they have great significance in the reconstruction of early metazoan evolution. Yet, the phylogeny and systematics of sponges are to some extent still unresolved, and there is an on-going debate about the exact branching pattern of their main clades and their relationships to the other non-bilaterian animals. Here, we review the current state of the deep phylogeny of sponges. Several studies have suggested that sponges are paraphyletic. However, based on recent phylogenomic analyses, we suggest that the phylum Porifera could well be monophyletic, in accordance with cladistic analyses based on morphology. This finding has many implications for the evolutionary interpretation of early animal traits and sponge development. We further review the contribution that mitochondrial genes and genomes have made to sponge phylogenetics and explore the current state of the molecular phylogenies of the four main sponge lineages (Classes), that is, Demospongiae, Hexactinellida, Calcarea, and Homoscleromorpha, in detail. While classical systematic systems are largely congruent with molecular phylogenies in the class Hexactinellida and in certain parts of Demospongiae and Homoscleromorpha, the high degree of incongruence in the class Calcarea still represents a challenge. We highlight future areas of research to fill existing gaps in our knowledge. By reviewing sponge development in an evolutionary and phylogenetic context, we support previous suggestions that sponge larvae share traits and complexity with eumetazoans and that the simple sedentary adult lifestyle of sponges probably reflects some degree of secondary simplification. In summary, while deep sponge phylogenetics has made many advances in the past years, considerable efforts are still required to achieve a comprehensive understanding of the relationships among and within the main sponge lineages to fully appreciate the evolution of this extraordinary metazoan phylum.

Sponge paraphyly and the origin of Metazoa

In order to allow critical evaluation of the interrelationships between the three sponge classes, and to resolve the question of mono- or paraphyly of sponges (Porifera), we used the polymerase chain reaction (PCR) to amplify almost the entire nucleic acid sequence of the 18S rDNA from several hexactinellid, demosponge and calcareous sponge species. The amplification products were cloned, sequenced and then aligned with previously reported sequences from other sponges and nonsponge metazoans and variously distant outgroups, and trees were constructed using both neighbour-joining and maximum parsimony methods. Our results suggest that sponges are paraphyletic, the Calcarea being more related to monophyletic Eumetazoa than to the siliceous sponges (Demospongiae, Hexactinellida). These results have important implications for our understanding of metazoan origins, because they suggest that the common ancestor of Metazoa was a sponge. They also have consequences for basal metazoan classification, implying that the phylum Porifera should be abandoned. Our results support the upgrading of the calcareous sponge class to the phylum level.

Phylogenetic Analyses Under Secondary Structure-Specific Substitution Models Outperform Traditional Approaches: Case Studies with Diploblast LSU

Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such nonindependent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a "doublet" model for pairing sites (rRNA-helices) and compared our findings with the results of "standard" approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.

Non-monophyly of most supraspecific taxa of calcareous sponges (Porifera, Calcarea) revealed by increased taxon sampling and partitioned Bayesian analysis of ribosomal DNA

Calcareous sponges (Porifera, Calcarea) play an important role for our understanding of early metazoan evolution, since several molecular studies suggested their closer relationship to Eumetazoa than to the other two sponge 'classes,' Demospongiae and Hexactinellida. The division of Calcarea into the subtaxa Calcinea and Calcaronea is well established by now, but their internal relationships remain largely unresolved. Here, we estimate phylogenetic relationships within Calcarea in a Bayesian framework, using full-length 18S and partial 28S ribosomal DNA sequences. Both genes were analyzed separately and in combination and were further partitioned by stem and loop regions, the former being modelled to take non-independence of paired sites into account. By substantially increasing taxon sampling, we show that most of the traditionally recognized supraspecific taxa within Calcinea and Calcaronea are not monophyletic, challenging the existing classification system, while monophyly of Calcinea and Calcaronea is again highly supported.

The fatty acids of calcareous sponges (Calcarea, Porifera)

Twenty-nine specimens of calcareous sponges (Class Calcarea, Phylum Porifera), covering thirteen representative species of the families Soleneiscidae, Leucaltidae, Levinellidae, Leucettidae, Clathrinidae, Sycettidae, Grantiidae, Jenkinidae, and Heteropiidae were analysed for their fatty acids. The fatty acids of Calcarea generally comprise saturated and monounsaturated linear (n-), and terminally methylated (iso-, anteiso-) C(14)-C(20) homologues. Furthermore, polyunsaturated C(22) fatty acids and the isoprenoic 4,8,12-trimethyltridecanoic acid were found. The most prominent compounds are n-C(16), iso-C(17), iso-C(18), n-C(18), n-C(20). In addition, a high abundance of the exotic 16-methyloctadecanoic acid (anteiso-C(19)) appears to be a characteristic trait of Calcarea. Long-chain 'demospongic acids', typically found in Demospongiae and Hexactinellida, are absent in Calcarea. The completely different strategy of calcarean fatty acid synthesis supports their phylogenetic distinctiveness from a common Demospongiae/Hexactinellida taxon. Both intraspecific and intraclass patterns of Calcarea showed great similarity, suggesting a conserved fatty acid composition that already existed in the last common ancestor of Calcinea and Calcaronea, i.e. before subclasses diverged.

Speculation with spiculation?—Three independent gene fragments and biochemical characters versus morphology in demosponge higher classification

Demosponge higher-level systematics is currently a subject of major changes due to the simplicity and paucity of complex morphological characters. Still, sponge classification is primarily based on morphological features. The systematics of the demosponge order Agelasida has been exceptionally problematic in the past. Here, we present the first molecular phylogenetic analysis based on three partially independent genes in demosponges in combination with a comprehensive search for biochemical synapomorphies to indicate their phylogenetic relationships. We show how sponges with fundamentally different skeletons can be in fact closely related and discuss examples of the misleading nature of morphological systematics in sponges.

Systematics and evolution of Demospongiae

Systematic and evolutionary studies of Demospongiae Sollas, 1885 are a very dynamic field of research. The scientific knowledge pertaining to Demospongiae systematics has been recently assembled in the collective book Systema Porifera. However, a general consensus among spongologists has not yet been achieved regarding this group and the phylogenetic relationships within Demospongiae and between Demospongiae and other clades of Porifera and metazoans are still unresolved. The two traditional subclasses Tetractinomorpha and Ceractinomorpha are polyphyletic and it is proposed that they be abandoned. Since the publication of Systema Porifera, several works have suggested the polyphyly of Halichondrida and the paraphyly of Haplosclerida, as well as the monophyly of Tetractinellida (Astrophorida + Spirophorida), Keratosa (Dictyoceratida + Dendroceratida), and Myxospongiae (Chondrosida + Verongida + Halisarcida). Within all the classical orders, whether they are monophyletic or not, families and even genera have also been found to be polyphyletic. For example, Ancorinidae, Geodiidae, and Axinellidae are clearly polyphyletic. No single data set is able to resolve all the problems; thus, it is absolutely necessary that the classification of Demospongiae be examined from all angles and with as many data sets as possible.

Embryogenesis and larval differentiation in sponges

Having descended from the first multicellular animals on earth, sponges are a key group in which to seek innovations that form the basis of the metazoan body plan, but sponges themselves have a body plan that is extremely difficult to reconcile with that of other animals. Adult sponges lack overt anterior–posterior polarity and sensory organs, and whether they possess true tissues is even debated. Nevertheless, sexual reproduction occurs as in other metazoans, with the development of embryos through a structured series of cellular divisions and organized rearrangements of cellular material, using both mesenchymal and epithelial movements to form a multicellular embryo. In most cases, the embryo undergoes morphogenesis into a spatially organized larva that has several cell layers, anterior–posterior polarity, and sensory capabilities. Here we review original data on the mode of cleavage, timing of cellular differentiation, and the mechanisms involved in the organization of differentiated cells to form the highly structured sponge larva. Our ultimate goal is to develop interpretations of the phylogenetic importance of these data within the Porifera and among basal Metazoa.

Sustainable use of marine resources: cultivation of sponges

Among all metazoan phyla, sponges are known to produce the largest number of bioactive compounds, some of them metabolites with human therapeutic value. Therefore, an increasing interest in basic cell biology research up to biochemical engineering can be observed aiming at the production of sponge metabolites under completely controlled conditions. One major obstacle is the limited availability of larger quantities of defined sponge material--the so-called supply problem. In this chapter, different approaches used so far for producing sponge biomass by in situ aquaculture as well as some significant progress in the maintenance of sponges in aquaria are reviewed. These approaches are mainly based on old methods for producing commercial bath sponges as well as on experience in maintaining sponges in public aquaria and on the usage of artificial substrates for a natural-like colonization structure. In recent years, great efforts have been made to set up in vitro culture systems for the cultivation of sponge cells. One of the major advantages of cell cultures is the possibility to control and manipulate the cultivation conditions depending on the sponge species and the target metabolite. Up to now, monolayer cultures of dissociated sponge cells have been shown in a few cases to produce the desired product. However, to date, no continuously growing sponge cell line has been established. Organotypic culture systems, which maintain or mimic the natural tissue structure, have been developed in recent years and demonstrate a promising way towards the biotechnology of sponges. Successful attempts to produce sponge metabolites using the three-dimensional growing primmorphs are given. The use of sponge fragments, another three-dimensional approach, has reappeared and has also been successfully used as an in vitro approach as well as for the biotechnological production of boreal sponge tissue.

Molecular phylogeny of Demospongiae: implications for classification and scenarios of character evolution

An analysis of the phylogenetic relationships of the 13 orders of Demospongiae, based on 18S and C1, D1 and C2 domains of 28S rRNA (for, respectively, 26 and 32 taxa) has been performed. The class Demospongiae as traditionally defined is not found to be monophyletic. Instead, a clade comprising all demosponges except Homoscleromorpha is well-supported, and we define phylogenetically the name Demospongiae in this more restricted sense to preclude the possibility of drastic alterations of the meaning of Demospongiae in the future, depending on the position of Homoscleromorpha. Within this clade Demospongiae s.s., ceractinomorphs and tetractinomorphs are polyphyletic, implying homoplastic evolution of characters such as reproductive strategies (viviparity vs. oviparity) and skeleton architecture (reticulate vs. radiate). The topology derived from our molecular data provides a basis for proposing a new classification of Demospongiae s.s., and suggests a reverse polarity of some characters, with respect to traditional conceptions: viviparity, presence of monaxon spicules and of spongin appear to be ancestral, whereas oviparity, and presence of tetraxon spicules appear as derived characters.

Reconstructing early sponge relationships by using the Burgess Shale fossil Eiffelia globosa, Walcott

The relationships of the sponge classes are controversial, particularly between the calcareous and siliceous sponges. Specimens of the putative calcarean Eiffelia globosa Walcott from the Burgess Shale show the presence of diagnostic hexactinellid spicules integrated into the skeletal mesh. The arrangement of these spicules in Eiffelia is shown to be precisely equivalent to that of early protospongioid hexactinellids, and sponge growth occurred through an identical pattern to produce identical skeletal body morphology. The difference in spicule composition of the classes is interpreted through the observation of taphonomic features of Eiffelia that suggest the presence of at least two mineralogically distinct layers within the spicules. These results support molecular analyses that identify the calcarean-silicisponge transition as the earliest major sponge branch and suggest that the heteractinids were paraphyletic with respect to the Hexactinellida.

Placozoa are not derived cnidarians: evidence from molecular morphology

The phylum Placozoa is represented by a single known species, Trichoplax adhaerens, a tiny marine organism that represents the most simple metazoan bauplan. Because of the latter, placozoans were originally considered the most basal metazoan phylum. A misinterpretation of the life cycle at the turn of the century and some more recent molecular phylogenetic analyses have placed Trichoplax as a derived species within the Cnidaria. The latter hypothesis assumes that the primitive organization of the Placozoa is the result of secondary reduction. Here we compare the molecular morphology of the predicted 16S rDNA structure and the mitochondrial genome between Trichoplax and representatives of all four cnidarian classes. Trichoplax shares a circular mtDNA molecule as a plesiomorphy with all other metazoans except for the derived cnidarian classes Hydrozoa, Scyphozoa, and Cubozoa. The predicted secondary structure of the 16S rRNA molecule differs substantially between Trichoplax and cnidarians, particularly with respect to the number and length of stem and loop regions. The new molecular morphological characters provide compelling evidence that Trichoplax is not a derived (medusozoan) cnidarian. Furthermore, it was found that the mitochondrial genome in Cubozoa consists of four linear molecules instead of a single circular molecule or two linear molecules, suggesting that the cubozoans may represent the most derived cnidarian group.

Clypeatula cooperensis gen. n., sp. n., a new freshwater sponge (Porifera, Spongillidae) from the Rocky Mountains of Montana, USA

A new genus and species of freshwater sponge, Clypeatula cooperensis, collected from three lakes in the Northern Rocky Mountains of Montana, USA, are described. The sponge grows as a hard, disc-shaped encrustation on the undersides of rocks and logs. It lacks microscleres and has amphioxeal megascleres that often show a slight midregion bulb and are usually covered with short, conical spines except at their tips. The sponge is also non-gemmulating, overwintering in a regressed state in which choanocyte chambers are reduced in number. Phylogenetic analyses of complete 18S rDNA sequences of C. cooperensis, Ephydatia muelleri, Spongilla lacustris and Eunapius fragilis suggest that C. cooperensis is more closely related to Ephydatia muelleri than to Spongilla lacustris or Eunapius fragilis. Our data, nonetheless, do not rule out the possibility that C. cooperensis is more closely related to the non-gemmulating sponges of Lake Baikal (Russia) than it is to Ephydatia muelleri. These phylogenetic analyses support the erection of a new genus, the monophyly of freshwater sponges belonging to the families Spongillidae and Lubomirskiidae, and the monophyly of demosponges.

Sphaeriid and corbiculid clams represent separate heterodont bivalve radiations into freshwater environments

Nine families of bivalve molluscs have undergone successful radiations in freshwater habitats, including three heterodont taxa: the Sphaeriidae, Corbiculidae, and Dreissenidae. Although the phylogenetic relationships of these freshwater heterodont families are controversial, most workers place the first two in the superfamily Corbiculoidea and assume that they represent a monophyletic grouping. We have tested competing phylogenetic hypotheses for the Corbiculoidea by constructing a representative molecular phylogeny, based on domains D1-D3 of the nuclear large subunit 28S rDNA, for 18 heterodont bivalves and for two oyster outgroup taxa. Our results do not support the monophyly of the Corbiculoidea and are consistent with the hypothesis that all three families of freshwater heterodonts represent independent colonization events by marine ancestors. Similarities in developmental mode specializations exhibited by some sphaeriids and corbiculids, such as sequential direct-developing broods, represent convergent adaptations to the freshwater environment. The corbiculid taxa form a clade with venerid and mactrid outgroups but we were not able to identify a putative marine outgroup for the sphaeriids.

Gene structure and function of tyrosine kinases in the marine sponge Geodia cydonium: autapomorphic characters in Metazoa

Porifera (sponges) represent the most ancient, extant metazoan phylum. They existed already prior to the 'Cambrian Explosion'. Based on the analysis of aa sequences of informative proteins, it is highly likely that all metazoan phyla evolved from only one common ancestor (monophyletic origin). As 'autapomorphic' proteins which are restricted to Metazoa only, integrin receptors, receptors with scavenger receptor cysteine-rich repeats, neuronal-like receptors and protein-tyrosine kinases (PTKs) have been identified in Porifera. From the marine sponge Geodia cydonium, a receptor tyrosine kinase (RTK) has been cloned that comprises the characteristic structural topology known from other metazoan RTKs; an extracellular domain, the transmembrane region, the juxtamembrane region and the TK domain. Only two introns, within the coding region of the RTK gene, could be found, which separate the two highly polymorphic immunoglobulin-like domains, found in the extracellular region of the enzyme. The functional role of this sponge RTK could be demonstrated both in situ (grafting experiments) and in vitro (increase of intracellular Ca2+ level). Upstream of this RTK gene, two further genes coding for tyrosine kinases (TK) have been identified. Both are intron-free. The deduced aa sequence of the first gene shows no transmembrane segment; from the second gene--so far--only half of its catalytic domain is known. A phylogenetic analysis with the TK domains from these sequences and a fourth, from a novel scavenger RTK (all domains comprise the signature for the TK class II receptors), showed that they are distantly related to the insulin and insulin-like receptors. The presented findings support the 'introns-late' hypothesis for such genes that encode 'metazoan' proteins. It is proposed that the TKs evolved from protein-serine/threonine kinases through modularization and subsequent exon shuffling. After formation of the ancestral TKs, the modules lost the framing introns to protect the evolutionary novelty. Since cell culture systems of sponges are now available, it can be expected that soon also those mechanisms that control the developmental programs will be unravelled.

Sponge phylogeny, animal monophyly, and the origin of the nervous system: 18S rRNA evidence

We sequenced 18S rRNA genes of a calcareous sponge, Clathrina cerebrum, a demosponge, Axinella polypoides, and a zoanthid cnidarian, Parazoanthus axinellae. Our phylogenetic analysis supports the monophyly of kingdom Animalia and confirms that choanoflagellate protozoans are their closest relatives. Sponges as a whole are monophyletic, but possibly paraphyletic; demosponges and hexactinellids form a monophyletic group of silicious sponges. Our phylogenetic trees support a monophyletic origin of the nervous system in the immediate common ancestor of Cnidaria and Ctenophora. They weakly suggest that animals with a nervous system may be more closely related to calcareous sponges than to silicious sponges; the nervous system might have originated in an early calcareous sponge. Our trees confirm that Myxozoa and Placozoa are animals that arose by secondary loss of the nervous system, but suggest that Myxozoa may be sisters of, rather than derived from, Bilateria. Kingdom Animalia is divided into four subkingdoms: Radiata (Porifera, Cnidaria, Placozoa, Ctenophora), Myxozoa, Mesozoa, and Bilateria. The 18S rRNA genes of Myxozoa evolved over twice as fast as in Radiata. Comparison with the fossil record reveals a brief 10-fold (or greater) acceleration in the rate of rRNA evolution in early Bilateria followed by normal low rates for about 500 million years.

Molecular phylogeny of Metazoa (animals): monophyletic origin

The phylogenetic relationships within the kingdom Animalia (Metazoa) have long been questioned. Focusing on the lowest eukaryotic multicellular organisms, the metazoan phylum Porifera (sponges), it remained unsolved if they evolved multicellularity independently from a separate protist lineage (polyphyly of animals) of derived from the same protist group as the other animal phyla (monophyly). After having analyzed genes typical for multicellularity (adhesion molecules/receptors and a nuclear receptor), we present evidence that Porifera should be placed in the kingdom Animalia. We therefore suggest a monophyletic origin for all animals.

The diversity of Malassezia yeasts confirmed by rRNA sequence and nuclear DNA comparisons

One hundred and four Malassezia strains (52 isolated from humans and 52 from animals) were compared using large subunit (LSU) ribosomal RNA sequence similarity and nuclear DNA complementarity. Eight groups of strains were recognized as genetically distinct species. Each taxon was confirmed by a homogeneous mole % GC and percentages of DNA/DNA reassociations higher than 85%. The non-lipid-dependent Malassezia yeasts were maintained as the unique taxon M. pachydermatis. In contrast, lipid-dependent strains were shown to be distributed among seven species: M. furfur, M. sympodialis and M. species 1-5. These taxa matched remarkably well with morphological and serological differences documented by previous investigators. The LSU rRNA sequences allowed a further intraspecific resolution with most of genomic taxa represented by several closely related sequences: M. pachydermatis counted up to seven sequences, M. furfur four sequences, M. species 1 comprised three sequences and M. species 2 and M. species 5 two sequences. Three species, M. sympodialis, M. species 3 and M. species 4, displayed a unique type of sequence. Thus, the present report demonstrates the usefulness of sequencing for both taxonomic and epidemiological purposes.

A palaeontological perspective

Palaeontology and molecular biology researchers need to develop a better dialogue. The recovery of biological information from Precambrian ecosystems that are thousands of millions of years old, the search for radical genomic reorganizations that might explain the irruption of groups with novel body plans, and the recovery of diagnostic molecules from fossils are all areas of active research, but communication between disciplines does not always occur.

Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons

The phylogeny of dermatophytes and dimorphic fungi was considered using the large-subunit of ribosomal RNA (25S rRNA). Aligned sequences of 595 nucleotides covering the two most divergent domains D1 and D2, permitted a comparison of phylogenetic relationships at different levels. The dimorphic species (Onygenaceae) were significantly separated from dermatophytes (Arthrodermataceae) and from a third group including geophilic or very weakly pathogenic species (Onygenaceae and Gymnoascaceae). On a species level, the varietal status of Histoplasma duboisii and Histoplasma farciminosum, as close relations of Histoplasma capsulatum, was confirmed. The dimorphic fungus Emmonsia parva, in spite of a completely different parasitic form (adiaspores instead of yeast-like cells), clustered with Blastomyces dermatitidis which has a perfect form resembling that of H. capsulatum. From our data, teleomorphs of E. parva, Paracoccidioides brasiliensis and H. farciminosum, three dimorphic fungi known only under their anamorphic states, should belong to the family of Onygenaceae and the genus Ajellomyces. Among Arthrodermataceae, and family containing the most keratinophilic species, it was not possible to establish a clear hierarchy of species. Only Ctenomyces serratus, the species adapted to degrade keratin of feathers, Trichophyton ajelloi and Trichophyton terrestre were significantly separated. The speciation of true dermatophytes resulted most likely from a very recent evolution by adaptation to parasitism. Among species used as outgroups, the two emerging pathogens Pseudallescheria boydii (Scedosporium apiospermum) and Scedosporium prolificans (Scedosporium inflatum) were shown to be closely related to each other.