Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa

The relationships at the base of the metazoan tree have been difficult to robustly resolve, and there are several different hypotheses regarding the interrelationships among sponges, cnidarians, ctenophores, placozoans, and bilaterians, with each hypothesis having different implications for the body plan of the last common ancestor of animals and the paleoecology of the late Precambrian. We have sequenced seven nuclear housekeeping genes from 17 new sponges, bringing the total to 29 species analyzed, including multiple representatives of the Demospongiae, Calcarea, Hexactinellida, and Homoscleromorpha, and analyzed a data set also including six nonmetazoan outgroups and 36 eumetazoans using a variety of phylogenetic methods and evolutionary models. We used leaf stability to identify rogue taxa and investigate their effect on the support of the nodes in our trees, and we identified clades most likely to represent phylogenetic artifacts through the comparison of trees derived using different methods (and models) and through site-stripping analyses. Further, we investigated compositional heterogeneity and tested whether amino acid composition bias affected our results. Finally, we used Bayes factors to compare our results against previously published phylogenies. All our maximum likelihood (ML) and Bayesian analyses find sponges to be paraphyletic, with all analyses finding three extant paraphyletic sponge lineages, Demospongiae plus Hexactinellida, Calcarea, and Homoscleromorpha. All but one of our ML and Bayesian analyses support the monophyly of Eumetazoa (here Cnidaria + Bilateria) and a sister group relationship between Placozoa (here Trichoplax adhaerens) and Eumetazoa. Bayes factors invariably provide decisive support in favor of poriferan paraphyly when compared against either a sister group relationship between Porifera and Cnidaria or with a monophyletic Porifera with respect to a monophyletic Eumetazoa. Although we were able to recover sponge monophyly using our data set, this was only possible under unrealistic evolutionary models, if poorly performing phylogenetic methods were used, or in situations where the potential for the generation of tree reconstruction artifacts was artificially exacerbated. Everything considered, our data set does not provide any support for a monophyletic Diploblastica (here Placozoa + Cnidaria + Porifera) and suggests that a monophyletic Porifera may be better seen as a phylogenetic artifact.

Shaping the things to come: ontogeny of lophotrochozoan neuromuscular systems and the tetraneuralia concept

Despite the large variation in adult bodyplan phenotypes, a worm-shaped morphology is considered plesiomorphic for both Lophotrochozoa and Bilateria. Although almost all larval and adult lophotrochozoan worms have serially arranged ring muscles in their body wall, a comparison of their ontogeny reveals no less than six different developmental pathways that lead to this homogenous arrangement of ring muscles. However, in all taxa, with the exception of chaetodermomorph molluscs and the segmented annelids, ring muscle development starts with synchronous formation of certain pioneer myocytes, which is thus considered basal for Lophotrochozoa. Recent studies on spiralian neurogenesis revealed remnants of ancestral segmentation in echiurans and sipunculans, thus confirming molecular phylogenetic studies that propose a close relationship of these three taxa. Larval entoprocts exhibit a mosaic of larval and adult molluscan characters and, among other apomorphies, share with polyplacophoran Mollusca a complex larval apical organ and a tetraneurous nervous system, strongly suggesting a monophyletic assemblage of Entoprocta and Mollusca. The term Tetraneuralia is proposed herein for this lophotrochozoan clade. Overall, formation of the lophotrochozoan neuromuscular bodyplan appears as a highly dynamic process on both the ontogenetic and the evolutionary timescales, highlighting the importance of insights into these processes for reconstructing ancestral bodyplan features and phylogenetic relationships.

The deep evolution of metazoan microRNAs

microRNAs (miRNAs) are approximately 22-nucleotide noncoding RNA regulatory genes that are key players in cellular differentiation and homeostasis. They might also play important roles in shaping metazoan macroevolution. Previous studies have shown that miRNAs are continuously being added to metazoan genomes through time, and, once integrated into gene regulatory networks, show only rare mutations within the primary sequence of the mature gene product and are only rarely secondarily lost. However, because the conclusions from these studies were largely based on phylogenetic conservation of miRNAs between model systems like Drosophila and the taxon of interest, it was unclear if these trends would describe most miRNAs in most metazoan taxa. Here, we describe the shared complement of miRNAs among 18 animal species using a combination of 454 sequencing of small RNA libraries with genomic searches. We show that the evolutionary trends elucidated from the model systems are generally true for all miRNA families and metazoan taxa explored: the continuous addition of miRNA families with only rare substitutions to the mature sequence, and only rare instances of secondary loss. Despite this conservation, we document evolutionary stable shifts to the determination of position 1 of the mature sequence, a phenomenon we call seed shifting, as well as the ability to post-transcriptionally edit the 5' end of the mature read, changing the identity of the seed sequence and possibly the repertoire of downstream targets. Finally, we describe a novel type of miRNA in demosponges that, although shows a different pre-miRNA structure, still shows remarkable conservation of the mature sequence in the two sponge species analyzed. We propose that miRNAs might be excellent phylogenetic markers, and suggest that the advent of morphological complexity might have its roots in miRNA innovation.

Complete mitochondrial genome of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata): phylogenetic position of Bryozoa and phylogeny of lophophorates within the Lophotrochozoa

BACKGROUND

The phylogenetic position of Bryozoa is one of the most controversial issues in metazoan phylogeny. In an attempt to address this issue, the first bryozoan mitochondrial genome from Flustrellidra hispida (Gymnolaemata, Ctenostomata) was recently sequenced and characterized. Unfortunately, it has extensive gene translocation and extremely reduced size. In addition, the phylogenies obtained from the result were conflicting, so they failed to assign a reliable phylogenetic position to Bryozoa or to clarify lophophorate phylogeny. Thus, it is necessary to characterize further mitochondrial genomes from slowly-evolving bryozoans to obtain a more credible lophophorate phylogeny.

RESULTS

The complete mitochondrial genome (15,433 bp) of Bugula neritina (Bryozoa, Gymnolaemata, Cheilostomata), one of the most widely distributed cheliostome bryozoans, is sequenced. This second bryozoan mitochondrial genome contains the set of 37 components generally observed in other metazoans, differing from that of F. hispida (Bryozoa, Gymnolaemata, Ctenostomata), which has only 36 components with loss of tRNAser(ucn) genes. The B. neritina mitochondrial genome possesses 27 multiple noncoding regions. The gene order is more similar to those of the two remaining lophophorate phyla (Brachiopoda and Phoronida) and a chiton Katharina tunicate than to that of F. hispida. Phylogenetic analyses based on the nucleotide sequences or amino acid residues of 12 protein-coding genes showed consistently that, within the Lophotrochozoa, the monophyly of the bryozoan class Gymnolaemata (B. neritina and F. hispida) was strongly supported and the bryozoan clade was grouped with brachiopods. Echiura appeared as a subtaxon of Annelida, and Entoprocta as a sister taxon of Phoronida. The clade of Bryozoa + Brachiopoda was clustered with either the clade of Annelida-Echiura or that of Phoronida + Entoprocta.

CONCLUSION

This study presents the complete mitochondrial genome of a cheliostome bryozoan, B. neritina. The phylogenetic analyses suggest a close relationship between Bryozoa and Brachiopoda within the Lophotrochozoa. However, the sister group of Bryozoa + Brachiopoda is still ambiguous, although it has some attractions with Annelida-Echiura or Phoronida + Entoprocta. If the latter is a true phylogeny, lophophorate monophyly including Entoprocta is supported. Consequently, the present results imply that Brachiozoa (= Brachiopoda + Phoronida) and the recently-resurrected Bryozoa concept comprising Ectoprocta and Entoprocta may be refuted.

Phylogenomics revives traditional views on deep animal relationships

The origin of many of the defining features of animal body plans, such as symmetry, nervous system, and the mesoderm, remains shrouded in mystery because of major uncertainty regarding the emergence order of the early branching taxa: the sponge groups, ctenophores, placozoans, cnidarians, and bilaterians. The "phylogenomic" approach [1] has recently provided a robust picture for intrabilaterian relationships [2, 3] but not yet for more early branching metazoan clades. We have assembled a comprehensive 128 gene data set including newly generated sequence data from ctenophores, cnidarians, and all four main sponge groups. The resulting phylogeny yields two significant conclusions reviving old views that have been challenged in the molecular era: (1) that the sponges (Porifera) are monophyletic and not paraphyletic as repeatedly proposed [4-9], thus undermining the idea that ancestral metazoans had a sponge-like body plan; (2) that the most likely position for the ctenophores is together with the cnidarians in a "coelenterate" clade. The Porifera and the Placozoa branch basally with respect to a moderately supported "eumetazoan" clade containing the three taxa with nervous system and muscle cells (Cnidaria, Ctenophora, and Bilateria). This new phylogeny provides a stimulating framework for exploring the important changes that shaped the body plans of the early diverging phyla.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background

There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum.

Results

The mitochondrial genome of P.esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups.

Conclusion

This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

Distinguishing heat from light in debate over controversial fossils

Fossil organisms offer our only direct insight into how the distinctive body plans of extant organisms were assembled. However, realizing the potential evolutionary significance of fossils can be hampered by controversy over their interpretation. Here, as a guide to evaluating palaeontological debates, we outline the process and pitfalls of fossil interpretation. The physical remains of controversial fossils should be reconstructed before interpreting homologies, and choice of interpretative model should be explicit and justified. Extinct taxa lack characters diagnostic of extant clades because the characters had not yet evolved, because of secondary loss, or because they have rotted away. The latter, if not taken into account, will lead to the spurious assignment of fossils to basally branching clades. Conflicting interpretations of fossils can often be resolved by considering all the steps in the process of anatomical analysis and phylogenetic placement, although we must accept that some fossil organisms are simply too incompletely preserved for their evolutionary significance to be realized.

DNA barcoding in Tardigrada: the first case study on Macrobiotus macrocalix Bertolani & Rebecchi 1993 (Eutardigrada, Macrobiotidae)

Morphological and molecular studies on a tardigrade species have been carried out to verify the possibility of using a DNA barcoding approach for species identification in this phylum. Macrobiotus macrocalix Bertolani & Rebecchi, 1993 was chosen as the test species since it belongs to a group of species in which the taxonomy is quite problematic. Animals and eggs belonging to three Italian and one Swedish populations have been investigated. Both morphological and molecular analyses show that all the populations belong to the same species. The low genetic distances recorded among the studied populations (0.3-1.0%) and the high genetic distance (15.9-16.3%) between these populations and a closely related species confirm the possibility of identifying a specimen of this species by its cytochrome oxidase subunit I sequence. Data from other authors support our results indicating that DNA barcoding can be applied to tardigrades. With our protocols, we have obtained voucher specimens that enable us to show a correspondence between morphology and molecular data.

The origins of multicellularity and the early history of the genetic toolkit for animal development

Multicellularity appeared early and repeatedly in life's history; its instantiations presumably required the confluence of environmental, ecological, and genetic factors. Comparisons of several independently evolved pairs of multicellular and unicellular relatives indicate that transitions to multicellularity are typically associated with increases in the numbers of genes involved in cell differentiation, cell-cell communication, and adhesion. Further examination of the DNA record suggests that these increases in gene complexity are the product of evolutionary innovation, tinkering, and expansion of genetic material. Arguably, the most decisive multicellular transition was the emergence of animals. Decades of developmental work have demarcated the genetic toolkit for animal multicellularity, a select set of a few hundred genes from a few dozen gene families involved in adhesion, communication, and differentiation. Examination of the DNA records of the earliest-branching animal phyla and their closest protist relatives has begun to shed light on the origins and assembly of this toolkit. Emerging data favor a model of gradual assembly, with components originating and diversifying at different time points prior to or shortly after the origin of animals.

Comparative larval myogenesis and adult myoanatomy of the rhynchonelliform (articulate) brachiopods Argyrotheca cordata, A. cistellula, and Terebratalia transversa

Background

Despite significant methodological progress, Brachiopoda remains one of the lophotrochozoan phyla for which no recent ontogenetic data employing modern methodologies such as fluorescence labelling and confocal microscopy are available. This is particularly astonishing given the ongoing controversy concerning its phylogenetic position. In order to contribute new morphogenetic data for phylogenetic and evolutionary inferences, we describe herein the ontogeny and myoanatomy of larvae and adults of the rhynchonelliform brachiopods Argyrotheca cordata, A. cistellula, and Terebratalia transversa using fluorescence F-actin labelling combined with confocal laserscanning microscopy.

Results

Fully grown larvae of A. cordata and T. transversa consist of three distinct body regions, namely an apical lobe, a mantle lobe with four bundles of setae, and a pedicle lobe. Myogenesis is very similar in these two species. The first anlagen of the musculature develop in the pedicle lobe, followed by setae muscles and the mantle lobe musculature. Late-stage larvae show a network of strong pedicle muscles, central mantle muscles, longitudinal muscles running from the mantle to the pedicle lobe, setae pouch muscles, setae muscles, a U-shaped muscle, serial mantle muscles, and apical longitudinal as well as apical transversal muscles. Fully developed A. cistellula larvae differ from the former species in that they have only two visible body lobes and lack setae. Nevertheless, we found corresponding muscle systems to all muscles present in the former two species, except for the musculature associated with the setae, in larvae of A. cistellula. With our survey of the adult myoanatomy of A. cordata and A. cistellula and the juvenile muscular architecture of T. transversa we confirm the presence of adductors, diductors, dorsal and ventral pedicle adjustors, mantle margin muscles, a distinct musculature of the intestine, and striated muscle fibres in the tentacles for all three species.

Conclusion

Our data indicate that larvae of rhynchonelliform brachiopods share a common muscular bodyplan and are thus derived from a common ancestral larval type. Comparison of the muscular phenotype of rhynchonelliform larvae to that of the other two lophophorate phyla, Phoronida and Ectoprocta, does not indicate homology of individual larval muscles. This may be due to an early evolutionary split of the ontogenetic pathways of Brachiopoda, Phoronida, and Ectoprocta that gave rise to the morphological diversity of these phyla.

Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes

Resolving the relationships among animal phyla is a key biological problem that remains to be solved. Morphology is unable to determine the relationships among most phyla and although molecular data have unveiled a new evolutionary scenario, they have their own limitations. Nuclear ribosomal genes (18S and 28S rDNA) have been used effectively for many years. However, they are considered of limited use for resolving deep divergences such as the origin of the bilaterians, due to certain drawbacks such as the long-branch attraction (LBA) problem. Here, we attempt to overcome these pitfalls by combining several methods suggested in previous studies and routinely used in contemporary standard phylogenetic analyses but that have not yet been applied to any bilaterian phylogeny based on these genes. The methods used include maximum likelihood and Bayesian inference, the application of models with rate heterogeneity across sites, wide taxon sampling and compartmentalized analyses for each problematic clade. The results obtained show that the combination of the above-mentioned methodologies minimizes the LBA effect, and a new Lophotrochozoa phylogeny emerges. Also, the Acoela and Nemertodermatida are confirmed with maximum support as the first branching bilaterians. Ribosomal RNA genes are thus a reliable source for the study of deep divergences in the metazoan tree, provided that the data are treated carefully.

Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothesis, and, with a lower statistical support, the paraphyly of Deuterostomia. These results, in particular the status of deuterostomes, need further confirmation, both through increased taxonomic sampling, and future improvements of probabilistic models.

The evolution of the Ecdysozoa

Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.

Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms and hemichordates as a sister grouping (Ambulacraria). Xenoturbellids are a relatively newly discovered phylum of worm-like deuterostomes that lacks a fossil record, but molecular evidence suggests that these animals are a sister group to the Ambulacraria. Within the chordates, cephalochordates share large stretches of chromosomal synteny with the vertebrates, have a complete Hox complex and are sister group to the vertebrates based on ribosomal and mitochondrial gene evidence. In contrast, tunicates have a highly derived adult body plan and are sister group to the vertebrates based on the analyses of concatenated genomic sequences. Cephalochordates and hemichordates share gill slits and an acellular cartilage, suggesting that the ancestral deuterostome also shared these features. Gene network data suggest that the deuterostome ancestor had an anterior-posterior body axis specified by Hox and Wnt genes, a dorsoventral axis specified by a BMP/chordin gradient, and was bilaterally symmetrical with left-right asymmetry determined by expression of nodal.

First maxillae suction discs in Branchiura (Crustacea): development and evolution in light of the first molecular phylogeny of Branchiura, Pentastomida, and other "Maxillopoda"

The fish ectoparasites Branchiura (Crustacea) display two different ways of attachment to the fish surface as adults: the first maxillae are either hooks (Dolops) or suction discs (Argulus, Chonopeltis, and Dipteropeltis). In larval Argulus foliaceus the first maxillae are hooks. With the first molecular phylogeny of the Branchiura as a background, the present paper discusses the evolutionary scenarios leading to hooks versus suction discs. Specific homologies exist between larval Argulus foliaceus hooks and adult Dolops ranarum hooks. These include the presence of a comparable number of segments/portions and a distal segment terminating in a double structure: a distal two-part hook (in Argulus) or one hook and an associate spine-like structure (in Dolops). In the phylogenetic reconstruction based on three molecular markers (mitochondrial 16S rRNA, nuclear 18S and 28S rRNA), Dolops ranarum is found to be in a sister group position to all other Branchiura, which in this analysis include six Argulus and one Chonopeltis sequences. Based on the molecular phylogeny a likely evolutionary scenario is that the ancestral branchiuran used hooks (on the first maxilla) for attachment, as seen in Dolops, of which the proximal part was subsequently modified into suction discs in Argulus and Chonopeltis (and Dipteropeltis). The sister group relationship of the Branchiura and Pentastomida is confirmed based on the most comprehensive taxon sampling until now. No evidence was found for a branchiuran in-group position of the Pentastomida.

Developmental expression of homeobox genes in the ctenophore Mnemiopsis leidyi

Homeobox genes are a large family of genes that encode helix-turn-helix transcription factors that play fundamental roles in such developmental processes including body axis formation and cell specification. They have been found in a wide variety of organisms, from fungi to plants and animals, with some classes being specific to the Metazoa. While it was once thought that organismal complexity was tied to gene complexity, sequencing of genomes from a cnidarian, poriferan, and placozoan have shown no clear correlation. However, little attention has been paid to ctenophores, another early branching taxon. Ctenophores are mostly pelagic marine animals, with complex morphological features, so understanding the gene content and expression of this nonbilaterian phylum is of key interest to evolutionary biology. Expression information from developmental genes in ctenophores is sparse. In this study, we isolated seven homeobox genes from the ctenophore Mnemiopsis leidyi and examined their expression through development. Phylogenetic analyses of these genes placed four in the ANTP class and three in the PRD class. These are the first reported full-length PRD class genes, although our analyses could not place them into specific families. We have found that most of these homeobox genes begin expression at gastrulation, and their expression patterns suggest a possible role in patterning of the tentacle apparati and pharynx.

Assembling the lophotrochozoan (=spiralian) tree of life

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.

Problematica old and new

Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.

Back in time: a new systematic proposal for the Bilateria

Conventional wisdom suggests that bilateral organisms arose from ancestors that were radially, rather than bilaterally, symmetrical and, therefore, had a single body axis and no mesoderm. The two main hypotheses on how this transformation took place consider either a simple organism akin to the planula larva of extant cnidarians or the acoel Platyhelminthes (planuloid-acoeloid theory), or a rather complex organism bearing several or most features of advanced coelomate bilaterians (archicoelomate theory). We report phylogenetic analyses of bilaterian metazoans using quantitative (ribosomal, nuclear and expressed sequence tag sequences) and qualitative (HOX cluster genes and microRNA sets) markers. The phylogenetic trees obtained corroborate the position of acoel and nemertodermatid flatworms as the earliest branching extant members of the Bilateria. Moreover, some acoelomate and pseudocoelomate clades appear as early branching lophotrochozoans and deuterostomes. These results strengthen the view that stem bilaterians were small, acoelomate/pseudocoelomate, benthic organisms derived from planuloid-like organisms. Because morphological and recent gene expression data suggest that cnidarians are actually bilateral, the origin of the last common bilaterian ancestor has to be put back in time earlier than the cnidarian-bilaterian split in the form of a planuloid animal. A new systematic scheme for the Bilateria that includes the Cnidaria is suggested and its main implications discussed.

Complete nucleotide sequences of mitochondrial genomes of two solitary entoprocts, Loxocorone allax and Loxosomella aloxiata: implications for lophotrochozoan phylogeny

The complete nucleotide sequences of the mitochondrial (mt) genomes of the entoprocts Loxocorone allax and Loxosomella aloxiata were determined. Both species carry the typical gene set of metazoan mt genomes and have similar organizations of their mt genes. However, they show differences in the positions of two tRNA(Leu) genes. Additionally, the tRNA(Val) gene, and half of the long non-coding region, is duplicated and inverted in the Loxos. aloxiata mt genome. The initiation codon of the Loxos. aloxiata cytochrome oxidase subunit I gene is expected to be ACG rather than AUG. The mt gene organizations in these two entoproct species most closely resemble those of mollusks such as Katharina tunicata and Octopus vulgaris, which have the most evolutionarily conserved mt gene organization reported to date in mollusks. Analyses of the mt gene organization in the lophotrochozoan phyla (Annelida, Brachiopoda, Echiura, Entoprocta, Mollusca, Nemertea, and Phoronida) suggested a close phylogenetic relationship between Brachiopoda, Annelida, and Echiura. However, Phoronida was excluded from this grouping. Molecular phylogenetic analyses based on the sequences of mt protein-coding genes suggested a possible close relationship between Entoprocta and Phoronida, and a close relationship among Brachiopoda, Annelida, and Echiura.

The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: evidence for programmed translational frameshifting

Background

Mitochondrial genomes (mtDNA) of numerous sponges have been sequenced as part of an ongoing effort to resolve the class-level phylogeny of the Porifera, as well as to place the various lower metazoan groups on the animal-kingdom tree. Most recently, the partial mtDNA of two glass sponges, class Hexactinellida, were reported. While previous phylogenetic estimations based on these data remain uncertain due to insufficient taxon sampling and accelerated rates of evolution, the mtDNA molecules themselves reveal interesting traits that may be unique to hexactinellids. Here we determined the first complete mitochondrial genome of a hexactinellid sponge, Aphrocallistes vastus, and compared it to published poriferan mtDNAs to further describe characteristics specific to hexactinellid and other sponge mitochondrial genomes.

Results

The A. vastus mtDNA consisted of a 17,427 base pair circular molecule containing thirteen protein-coding genes, divergent large and small subunit ribosomal RNAs, and a reduced set of 18 tRNAs. The A. vastus mtDNA showed a typical hexactinellid nucleotide composition and shared a large synteny with the other sequenced glass sponge mtDNAs. It also contained an unidentified open reading frame and large intergenic space region. Two frameshifts, in the cox3 and nad6 genes, were not corrected by RNA editing, but rather possessed identical shift sites marked by the extremely rare tryptophan codon (UGG) followed by the common glycine codon (GGA) in the +1 frame.

Conclusion

Hexactinellid mtDNAs have shown similar trends in gene content, nucleotide composition, and codon usage, and have retained a large gene syntenty. Analysis of the mtDNA of A. vastus has provided evidence diagnostic for +1 programmed translational frameshifting, a phenomenon disparately reported throughout the animal kingdom, but present in the hexactinellid mtDNAs that have been sequenced to date.

Extracellular matrix production and calcium carbonate precipitation by coral cells in vitro

The evolution of multicellularity in animals required the production of extracellular matrices that serve to spatially organize cells according to function. In corals, three matrices are involved in spatial organization: (i) an organic ECM, which facilitates cell-cell and cell-substrate adhesion; (ii) a skeletal organic matrix (SOM), which facilitates controlled deposition of a calcium carbonate skeleton; and (iii) the calcium carbonate skeleton itself, which provides the structural support for the 3D organization of coral colonies. In this report, we examine the production of these three matrices by using an in vitro culturing system for coral cells. In this system, which significantly facilitates studies of coral cell physiology, we demonstrate in vitro excretion of ECM by primary (nondividing) tissue cultures of both soft (Xenia elongata) and hard (Montipora digitata) corals. There are structural differences between the ECM produced by X. elongata cell cultures and that of M. digitata, and ascorbic acid, a critical cofactor for proline hydroxylation, significantly increased the production of collagen in the ECM of the latter species. We further demonstrate in vitro production of SOM and extracellular mineralized particles in cell cultures of M. digitata. Inductively coupled plasma mass spectrometry analysis of Sr/Ca ratios revealed the particles to be aragonite. De novo calcification was confirmed by following the incorporation of (45)Ca into acid labile macromolecules. Our results demonstrate the ability of isolated, differentiated coral cells to undergo fundamental processes required for multicellular organization.

Hox, Wnt, and the evolution of the primary body axis: insights from the early-divergent phyla

The subkingdom Bilateria encompasses the overwhelming majority of animals, including all but four early-branching phyla: Porifera, Ctenophora, Placozoa, and Cnidaria. On average, these early-branching phyla have fewer cell types, tissues, and organs, and are considered to be significantly less specialized along their primary body axis. As such, they present an attractive outgroup from which to investigate how evolutionary changes in the genetic toolkit may have contributed to the emergence of the complex animal body plans of the Bilateria. This review offers an up-to-date glimpse of genome-scale comparisons between bilaterians and these early-diverging taxa. Specifically, we examine these data in the context of how they may explain the evolutionary development of primary body axes and axial symmetry across the Metazoa. Next, we re-evaluate the validity and evolutionary genomic relevance of the zootype hypothesis, which defines an animal by a specific spatial pattern of gene expression. Finally, we extend the hypothesis that Wnt genes may be the earliest primary body axis patterning mechanism by suggesting that Hox genes were co-opted into this patterning network prior to the last common ancestor of cnidarians and bilaterians.

MAPK activation and the specification of the D quadrant in the gastropod mollusc, Crepidula fornicata

Embryos of the gastropod snail Crepidula fornicata exhibit a typical spiral cleavage pattern. Although a small polar lobe is formed at the first and second cleavage divisions, the embryo of C. fornicata exhibits a mode of development similar to that of equal-cleaving spiralians in which the D quadrant is conditionally specified by inductive interactions involving the derivatives of the first quartet micromeres. This study demonstrates that mitogen activated protein kinases, MAPK, are initially activated in the progeny of the first quartet micromeres, just prior to the birth of the third quartet (e.g., late during the 16-cell and subsequently during the 20-cell stages). Afterwards, MAPK is activated in 3D just prior to the 24-cell stage, transiently in 4d and finally in a subset of animal micromeres immediately following those stages. This pattern of MAPK activation differs from that reported for other spiralians. Using an inhibitor of MAPK kinase (MEK), we demonstrated that activated MAPK is required for the specification of the 3D macromere, during the late 16-cell through early 24-cell stages. This corresponds to the interval when the progeny of the first quartet micromeres specify the D quadrant macromere. Activated MAPK is not required in 3D later during the 24-cell stage or in the embryonic organizer, 4d, for its normal activity. Likewise, activated MAPK is not required in the animal micromeres during subsequent stages of development. Additional experiments suggest that the polar lobe, though not required for normal development, may play a role in restricting the activation of MAPK and biasing the specification of the 3D macromere.

Annulonemertes (phylum Nemertea): when segments do not count

We estimated the phylogenetic position of the pseudosegmented ribbon worm Annulonemertes minusculus to test proposed evolutionary hypotheses to explain these body constrictions. The analysis is based on 18S rDNA sequences and shows that the species belongs to an apomorphic clade of hoplonemertean species. The segmentation has no phylogenetic bearing as previously discussed, but is a derived character probably coupled to the species' interstitial habitat.

The tardigrade Hypsibius dujardini, a new model for studying the evolution of development

Studying development in diverse taxa can address a central issue in evolutionary biology: how morphological diversity arises through the evolution of developmental mechanisms. Two of the best-studied developmental model organisms, the arthropod Drosophila and the nematode Caenorhabditis elegans, have been found to belong to a single protostome superclade, the Ecdysozoa. This finding suggests that a closely related ecdysozoan phylum could serve as a valuable model for studying how developmental mechanisms evolve in ways that can produce diverse body plans. Tardigrades, also called water bears, make up a phylum of microscopic ecdysozoan animals. Tardigrades share many characteristics with C. elegans and Drosophila that could make them useful laboratory models, but long-term culturing of tardigrades historically has been a challenge, and there have been few studies of tardigrade development. Here, we show that the tardigrade Hypsibius dujardini can be cultured continuously for decades and can be cryopreserved. We report that H. dujardini has a compact genome, a little smaller than that of C. elegans or Drosophila, and that sequence evolution has occurred at a typical rate. H. dujardini has a short generation time, 13-14 days at room temperature. We have found that the embryos of H. dujardini have a stereotyped cleavage pattern with asymmetric cell divisions, nuclear migrations, and cell migrations occurring in reproducible patterns. We present a cell lineage of the early embryo and an embryonic staging series. We expect that these data can serve as a platform for using H. dujardini as a model for studying the evolution of developmental mechanisms.

Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation

Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this method to the analysis of animal phylogeny, obtained support for an Ecdysozoa clade (Roy SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408). The critical assumption in the method was the independence of intron loss in different branches of the phylogenetic tree. Here, this assumption is refuted by showing that the branch-specific intron loss rates are strongly correlated. We show that different tree topologies are obtained, in each case with a significant statistical support, when different subsets of intron positions are analyzed. The analysis of the conserved intron positions supports the Coelomata topology, that is, a clade comprised of arthropods and chordates, whereas the analysis of more variable intron positions favors the Ecdysozoa topology, that is, a clade of arthropods and nematodes. We show, however, that the support for Ecdysozoa is fully explained by parallel loss of introns in nematodes and arthropods, a factor that does not contribute to the analysis of the conserved introns. The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems.

Stability of characters and construction of phylogenetic trees

Parsimony methods infer phylogenetic trees by minimizing number of character changes required to explain observed character states. From the perspective of applicability of parsimony methods, it is important to assess whether the characters used to infer phylogeny are likely to provide a correct tree. We introduce a graph theoretical characterization that helps to assess whether given set of characters is appropriate to use with parsimony methods. Given a set of characters and a set of taxa, we construct a network called character overlap graph. We show that the character overlap graph for characters that are appropriate to use in parsimony methods is characterized by significant under-representation of subnetworks known as holes, and provide a validation for this observation. This characterization explains success in constructing evolutionary trees using parsimony method for some characters (e.g., protein domains) and lack of such success for other characters (e.g., introns). In the latter case, the understanding of obstacles to applying parsimony methods in a direct way has lead us to a new approach for detecting inconsistent and/or noisy data. Namely, we introduce the concept of stable characters which is similar but less restrictive than the well known concept of pairwise compatible characters. Application of this approach to introns produces the evolutionary tree consistent with the Coelomata hypothesis.

EST sequencing of Onychophora and phylogenomic analysis of Metazoa

Onychophora (velvet worms) represent a small animal taxon considered to be related to Euarthropoda. We have obtained 1873 5' cDNA sequences (expressed sequence tags, ESTs) from the velvet worm Epiperipatus sp., which were assembled into 833 contigs. BLAST similarity searches revealed that 51.9% of the contigs had matches in the protein databases with expectation values lower than 10(-4). Most ESTs had the best hit with proteins from either Chordata or Arthropoda (approximately 40% respectively). The ESTs included sequences of 27 ribosomal proteins. The orthologous sequences from 28 other species of a broad range of phyla were obtained from the databases, including other EST projects. A concatenated amino acid alignment comprising 5021 positions was constructed, which covers 4259 positions when problematic regions were removed. Bayesian and maximum likelihood methods place Epiperipatus within the monophyletic Ecdysozoa (Onychophora, Arthropoda, Tardigrada and Nematoda), but its exact relation to the Euarthropoda remained unresolved. The "Articulata" concept was not supported. Tardigrada and Nematoda formed a well-supported monophylum, suggesting that Tardigrada are actually Cycloneuralia. In agreement with previous studies, we have demonstrated that random sequencing of cDNAs results in sequence information suitable for phylogenomic approaches to resolve metazoan relationships.

Acoel flatworms are not platyhelminthes: evidence from phylogenomics

Acoel flatworms are small marine worms traditionally considered to belong to the phylum Platyhelminthes. However, molecular phylogenetic analyses suggest that acoels are not members of Platyhelminthes, but are rather extant members of the earliest diverging Bilateria. This result has been called into question, under suspicions of a long branch attraction (LBA) artefact. Here we re-examine this problem through a phylogenomic approach using 68 different protein-coding genes from the acoel Convoluta pulchra and 51 metazoan species belonging to 15 different phyla. We employ a mixture model, named CAT, previously found to overcome LBA artefacts where classical models fail. Our results unequivocally show that acoels are not part of the classically defined Platyhelminthes, making the latter polyphyletic. Moreover, they indicate a deuterostome affinity for acoels, potentially as a sister group to all deuterostomes, to Xenoturbellida, to Ambulacraria, or even to chordates. However, the weak support found for most deuterostome nodes, together with the very fast evolutionary rate of the acoel Convoluta pulchra, call for more data from slowly evolving acoels (or from its sister-group, the Nemertodermatida) to solve this challenging phylogenetic problem.

Molecular phylogenetics in Hydra, a classical model in evolutionary developmental biology

Among the earliest diverging animal phyla are the Cnidaria. Freshwater polyps of the genus Hydra (Cnidaria, Hydrozoa) have long been of general interest because different species of Hydra reveal fundamental principles that underlie development, differentiation, regeneration and also symbiosis. The phylogenetic relationships among the Hydra species most commonly used in current research are not resolved yet. Here we estimate the phylogenetic relations among eight scientifically important members of the genus Hydra with molecular data from two nuclear (18S rDNA, 28S rDNA) and two mitochondrial (16S rRNA, cytochrome oxidase subunit I (COI)) genes. The phylogenetic trees obtained by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods were generally compatible with present morphological classification patterns. However, the present analysis also bears on several long-standing questions about Hydra systematics and reveals some characteristics of the phylogenetic relationships of this genus that were unknown so far. It indicates that Hydra viridissima, the only species in Hydra, which contains symbiotic algae, might be considered as the sister group to all other species within this genus. Analyses of both nuclear and mitochondrial sequences support the view that Hydra oligactis and Hydra circumcincta are sisters to all other Hydra species. Unexpectedly, we also find that in contrast to its initial description, the strain used for making transgenic Hydra, Hydra vulgaris (strain AEP) is more closely related to Hydra carnea than to other species of Hydra.

A new look at the ventral nerve centre of Sagitta: implications for the phylogenetic position of Chaetognatha (arrow worms) and the evolution of the bilaterian nervous system

BACKGROUND

The Chaetognatha (arrow worms) are a group of marine carnivores whose phylogenetic relationships are still vigorously debated. Molecular studies have as yet failed to come up with a stable hypothesis on their phylogenetic position. In a wide range of metazoans, the nervous system has proven to provide a wealth of characters for analysing phylogenetic relationships (neurophylogeny). Therefore, in the present study we explored the structure of the ventral nerve centre ("ventral ganglion") in Sagitta setosa with a set of histochemical and immunohistochemical markers.

RESULTS

In specimens that were immunolabeled for acetylated-alpha tubulin the ventral nerve centre appeared to be a condensed continuation of the peripheral intraepidermal nerve plexus. Yet, synapsin immunolocalization showed that the ventral nerve centre is organized into a highly ordered array of ca. 80 serially arranged microcompartments. Immunohistochemistry against RFamide revealed a set of serially arranged individually identifiable neurons in the ventral nerve centre that we charted in detail.

CONCLUSION

The new information on the structure of the chaetognath nervous system is compared to previous descriptions of the ventral nerve centre which are critically evaluated. Our findings are discussed with regard to the debate on nervous system organisation in the last common bilaterian ancestor and with regard to the phylogenetic affinities of this Chaetognatha. We suggest to place the Chaetognatha within the Protostomia and argue against hypotheses which propose a deuterostome affinity of Chaetognatha or a sister-group relationship to all other Bilateria.