The origin of annelids

Annelids are a phylum of segmented bilaterian animals that have become important components of ecosystems spanning terrestrial realms to the deep sea. Annelids are remarkably diverse, possessing high taxonomic diversity and exceptional morphological disparity, and have evolved numerous feeding strategies and ecologies. Their interrelationships and evolution have been the source of much controversy over the past century with the composition of the annelid crown group, the relationship of major groups and the body plan of the ancestral annelid having undergone major recent revisions. There is a convincing body of molecular evidence that polychaetes form a paraphyletic grade and that clitellates are derived polychaetes. The earliest stem group annelids from Cambrian Lagerstätten are errant, epibenthic polychaetes, confirming that biramous parapodia, head appendages and diverse, simple chaetae are primitive for annelids. Current evidence from molecular clocks and the fossil record suggest that crown group annelids are a Late Cambrian – Ordovician radiation, with clitellates radiating in the Late Palaeozoic. Their body fossil record is largely confined to deposits showing exceptional preservation and is punctuated by the acquisition of hard parts in major groups. The discovery of an Ordovician fossil with soft tissues has shown that machaeridians are in fact a clade of crown polychaetes. They were in existence for more than 200 million years and possess unique calcitic dorsal armour, allowing their mode of life and phylogeny to be interpreted in the context of the annelid body plan. We identify a novel clade of machaeridians, the Cuniculepadida, which exhibit a series of adaptations for burrowing.     

Protonephridia and Metanephridia - their relation within the Bilateria

Two different kinds of nephridia occur within the Bilateria, protonephridia closed up by a terminal cell and metanephridia opening into the coelomic cavity. Both initially filter and subsequently modify intercellular fluids. Whereas metanephridia are strictly correlated to a coelom, proto-nephria occur in acoelomate as well as in coelomate organisms. Protonephridia of different bilaterian taxa correspond to each other in several structural features. Therefore, it is hypothesized that protonephridia are homologous organs throughout the Bilateria. They must have evolved once as one pair of monociliated organs orinatinng from the ectoderm and consistin of one terminal, one duct and one nephropore cell In the ground pattern of the Bilateria the cilium of the terminal cell has only one rootlet and is surrounded by resumably eight strengthened and elongated microvilli. Cilium and microvilli extend into the hollow cyinder of the terminal cell, which is oriented distally and is attached to the adjacent duct cell by desmosomes. This cylinder is perforated by clefts and represents the supporting structure of the filtration barrier consisting of extracellular matrix. In the Annelida and Phoronida, the metanehridia at the postlarval stages are ontogenetically preceded by protonephridia in the larva, but far reaching structural and developmental differ ences exist between the metanephridia of both. In horonids the rotonephrdial duct of the larva is retained in the postlarva and acquires a coelothelially derived funnel, whereas in annelids the metanephridia are uniform organs orihating from a solid anlage, which is a repetition of the protonehridial anlage of the larva. The differences contradict a homology of the metanephridia in Annegda and Phoronida. We therefore have to conclude that metanephridia must have evolved indeendently, at least two times. The comparative analysis of nephridia in the Bilateria allows the following hyothesis: Pro tonephridia were evolved in a monohasic acoelomate organism in the stem fineage of the Bilateria. During the evolution of biphasic life cycles consisting of an acoelomate larva and a coelomate adult, the information about the differentiation of protonephridia has been preserved in the early acoelomate developmental (larval) stages. During postlarval development and the formation of a coelom the protonephridia have either been retained or modified into meta nephridia. Accordin to the differences between the metanehridia of phoronids and annelids, we emphasize that. tiere is no possibility to trace back all bilaterian taxa with a coelom to a common stem species.     

Current status of annelid phylogeny

Annelida is an ecologically and morphologically diverse phylum within the Lophotrochozoa whose members occupy a wide range of environments and show diverse life styles. The phylogeny of this group comprising more than 17,000 species remained controversial for a long time. By using next-generation sequencing and phylogenomic analyses of huge data matrices, it was finally possible to reach a well-supported and resolved annelid backbone tree. Most annelid diversity is comprised in two reciprocal monophyletic groups, Sedentaria and Errantia, which are named after the predominant life style of their members. Errantia include Aciculata (Phyllodocida?+?Eunicida) and Protodriliformia, which is a taxon of interstitial polychaetes. Sedentaria comprise most of the polychaete families formerly classified as Canalipalpata or Scolecida, as well as the Clitellata. Six taxa branch as a basal grade outside of this major radiation: Oweniidae, Magelonidae, Chaetopteridae, Sipuncula, Amphinomida, and Lobatocerebrum. Oweniidae and Magelonidae form a monophyletic group which we name Palaeoannelida, which constitutes the sister taxon of the remaining annelids. The early splits of annelid phylogeny date back to the Cambrian. The new annelid phylogeny highlights the variability and lability of annelid body plans, and many instances of simplifications of body plan as adaptations to new life styles can be found. Therefore, annelids will be an appropriate model to understand major transitions in the evolution of Bilateria in general. Evolutionary developmental studies are one way to investigate macroevolutionary transition in annelids. We briefly summarize the state of developmental model organisms in Annelida and also propose new candidates on the background of the phylogeny.     

Precambrian trace fossils and the rise of bilaterian animals

In this attempt to synthesize present knowledge into a coherent story, the Cambrian explosion is interpreted to represent a true adaptive radiation, an event similar to Phanerozoic radiation events in principle but unique in its possibilities. A model of bilaterian evolution helps explain how this particular event involved the sudden initiation of major coelomate phyla. In many of these groups, preservable skeletons are part of the basic body plan. Biochemical‐sequence analyses indicate that acoelomates and pseudocoelomates branched off long before the coelomate radiation. The great differences between Vendian and Cambrian ichnofaunas, therefore, may be the result of a major shift in composition from Vendian acoelomate‐pseudocoelomate‐procoelomate faunas to Phanerozoic faunas dominated by new coelomate groups.     

Myoanatomy of Myzostoma cirriferum (Annelida,Myzostomida): Implications for the evolution of the myzostomid body plan

Studies of rare genomic marker systems suggest that Myzostomida are a subgroup of Annelida and phylogenomic analyses indicate an early divergence of this taxon within annelids. However, adult myzostomids show a highly specialized body plan, which lacks typical annelid features, such as external body annulation, coelomic cavities with metanephridia, and segmental ganglia of the nervous system. The putative loss of these features might be due to the parasitic/symbiotic lifestyle of myzostomids associated with echinoderms. In contrast, the larval anatomy and adult locomotory system resemble those of annelids. To clarify whether the myoanatomy of myzostomids reflects their relationship to annelids, we analyzed the distribution of f‐actin, a common component of muscle fibers, in specimens of Myzostoma cirriferum using phalloidin‐rhodamine labeling in conjunction with confocal laser‐scanning microscopy. Our data reveal that the musculature of the myzostomid body comprises an outer circular layer, an inner longitudinal layer, numerous dorsoventral muscles, and prominent muscles of the parapodial complex. These features correspond well with the common organization of the muscular system in Annelida. In contrast to other annelids, however, several elements of the muscular system in M. cirriferum, including the musculature of the body wall, and the parapodial flexor muscles, exhibit radial symmetry overlaying a bilateral body plan. These findings are in line with the annelid affinity of myzostomids and suggest that the apparent partial radial symmetry of M. cirriferum arose secondarily in this species. Based on our data, we provide a scenario on the rearrangements of muscle fibers that might have taken place in the lineage leading to this species. J. Morphol., 2013. © 2012 Wiley Periodicals, Inc.     

Distribution of segment regeneration ability in the Annelida

The annelids are an excellent group in which to investigatethe evolution of regeneration abilities. They exhibit qualitativeand quantitative variation in regeneration ability, includingamong closely related species, and their segmental body organizationmakes comparing results among species relatively straightforward.Here, I compile information on the presence/absence of segmentregeneration ability across the annelids. The ability to regenerateposteriorly appears to be nearly universal in the annelids.It is almost certainly ancestral for the phylum and may havebeen lost only a few times. The ability to regenerate anteriorlyis common but less widespread. It is absent in about a dozengroups, almost surely representing multiple independent lossesof this ability. Several non-regenerating species are closelyrelated to regenerating species, indicating very recent losses(or gains). Despite the fact that lack of this ability is unusual,there is a publication bias against reporting the lack of regenerationability, and in many cases the judgment that a particular speciesis unable to regenerate is based on incomplete or unpublisheddata. Thus, in order to build rigorous frameworks for futurecomparative studies of annelid regeneration, there is a needfor published studies clearly documenting the lack of regenerationabilities in annelid species. The review of regeneration datapresented here is especially useful in highlighting annelidgroups that possess both regenerating and non-regenerating representatives.Investigations of these groups may be particularly useful forelucidating the mechanisms leading to the loss (or perhaps gain)of segment regeneration ability.     

Unsegmented annelids? Possible origins of four lophotrochozoan worm taxa

In traditional classification schemes, the Annelida consists of the Polychaeta and the Clitellata (the latter including the Oligochaeta and Hirudinida). However, recent analyses suggest that annelids are much more diverse than traditionally believed, and that polychaetes are paraphyletic. Specifically, some lesser-known taxa (previously regarded as separate phyla) appear to fall within the annelid radiation. Abundant molecular, developmental, and morphological data show that the Siboglinidae, which includes the formerly recognized Pogonophora and Vestimentifera, are derived annelids; recent data from the Elongation Factor-1α (EF-1α) gene also suggest that echiurids are of annelid ancestry. Further, the phylogenetic origins of two other lesser-known groups of marine worms, the Myzostomida and Sipuncula, have recently been called into question. Whereas some authors advocate annelid affinities, others argue that these taxa do not fall within the annelid radiation. With advances in our understanding of annelid phylogeny, our perceptions of body plan evolution within the Metazoa are changing. The evolution of segmentation probably is more plastic than traditionally believed. However, as our understanding of organismal evolution is being revised, we are also forced to reconsider the specific characters being examined. Should segmentation be considered a developmental process or an ontological endpoint?     

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.     

Direction of evolution within Annelida and the definition of Pleistoannelida

The direction of evolution within Annelida has been a long and contentious debate since the middle of the last century. Based on functional morphology two hypotheses were predominantly discussed. The first hypothesis proposed an earthworm‐like ancestor and the evolution of a segmented coelom as an aid for peristaltic burrowing, whereas the second one postulated that the ancestral annelid resembled more an errant polychaete and the segmented coelom evolved as a requirement for blood transportation to the parapodia. A recent phylogenomic study of annelids as well as new fossil records of early annelids provide new insights to this debate, which will be discussed in this paper. Based on these data the ancestral annelid is most likely a mixture of sedentary and errant annelid features indicating an evolutionary origin of Annelida as a microphagous surface deposit‐feeder crawling upon and through soft‐bottom habitats. Hence, the evolution of iterative parapodia as locomotive devices most likely drove the evolution of segmentation in Annelida. Moreover, as Struck et al. (2011) did not provide a proper definition and name for their clade 1 this clade shall be named Pleistoannelida and is defined by the last common ancestor of Sedentaria and Errantia sensu Struck et al. (2011), and all the descendants of that ancestor.     

Parasegmental appendage allocation in annelids and arthropods and the homology of parapodia and arthropodia

The new animal phylogeny disrupts the traditional taxon Articulata (uniting arthropods and annelids) and thus calls into question the homology of the body segments and appendages in the two groups. Recent work in the annelid Platynereis dumerilii has shown that although the set of genes involved in body segmentation is similar in the two groups, the body units of annelids correspond to arthropod parasegments not segments. This challenges traditional ideas about the homology of "segmental" organs in annelids and arthropods, including their appendages. Here I use the expression of engrailed, wingless and Distal-less in the arthropod Artemia franciscana to identify the parasegment boundary and the appendage primordia. I show that the early body organization including the appendage primordia is parasegmental and thus identical to the annelid organization and by deriving the different adult appendages from a common ground plan I suggest that annelid and arthropod appendages are homologous structures despite their different positions in the adult animals. This also has implications for the new animal phylogeny, because it suggests that Urprotostomia was not only parasegmented but also had parasegmental appendages similar to extant annelids, and that limb-less forms in the Protostomia are derived from limb-bearing forms.     

Annelid phylogeny and the status of Sipuncula and Echiura

Background  

Annelida comprises an ancient and ecologically important animal phylum with over 16,500 described species and members are the dominant macrofauna of the deep sea. Traditionally, two major groups are distinguished: Clitellata (including earthworms, leeches) and "Polychaeta" (mostly marine worms). Recent analyses of molecular data suggest that Annelida may include other taxa once considered separate phyla (i.e., Echiura, and Sipuncula) and that Clitellata are derived annelids, thus rendering "Polychaeta" paraphyletic; however, this contradicts classification schemes of annelids developed from recent analyses of morphological characters. Given that deep-level evolutionary relationships of Annelida are poorly understood, we have analyzed comprehensive datasets based on nuclear and mitochondrial genes, and have applied rigorous testing of alternative hypotheses so that we can move towards the robust reconstruction of annelid history needed to interpret animal body plan evolution.     

An Early Cambrian stem polychaete with pygidial cirri

The oldest annelid fossils are polychaetes from the Cambrian Period. They are representatives of the annelid stem group and thus vital in any discussion of how we polarize the evolution of the crown group. Here, we describe a fossil polychaete from the Early Cambrian Sirius Passet fauna, Pygocirrus butyricampum gen. et sp. nov., with structures identified as pygidial cirri, which are recorded for the first time from Cambrian annelids. The body is slender and has biramous parapodia with chaetae organized in laterally oriented bundles. The presence of pygidial cirri is one of the characters that hitherto has defined the annelid crown group, which diversified during the Cambrian-Ordovician transition. The newly described fossil shows that this character had already developed within the total group by the Early Cambrian.     

Ultrastructure of the body cavity lining in a secondary acoelomate,Microphthalmus cf. Listensis westheide (Polychaeta: Hesionidae)

The organization of the body cavity lining in selected regions of the juvenile and adult of the interstitial hesionid polychaete Microphthalmus cf. listensis is described. Tissues comprising the body cavity lining in the juvenile consist of somatic and splanchnic circular and longitudinal muscles and undifferentiated cells. Somatic and splanchnic cell layers exhibit epithelial ( = eucoelomate) organization in the pharyngeal region. In the midbody, some undifferentiated cells exhibiting mesenchymal organization persist among the epithelially organized somatic and splanchnic cells, forming a gradation between eucoelomate and acoelomate tissue organizations. A coelomic cavity is absent. Tissues comprising the body cavity lining of the adult consist of somatic and splanchnic circular and longitudinal myocytes and coelenchymal cells. Coelenchymal cells are shown from serial section analysis to be mesenchymal in organization and derived from the somatic peritoneum. A 30–65-nm coelomic cavity lies between the apices of somatic and splanchnic cell layers in the pharyngeal region. In the anterior setigerous segments, the coelom is reduced to a narrow cavity surrounded by coelenchymal cells lying midventrally between the paired ejaculatory ducts. There is a regional obliteration of the splanchnic musculature in the posterior segments so that apices of the coelenchymal cells lie in direct apposition to the basal extracellular matrix of the gut. The coeom is only present middorsally as a 0.7-μm-wide cavity. Although the coelomic cavity is highly reduced in the adult, the body cavity lining still reveals its origin from the epithelial ( = eucoelomate) organization. The findings of this study illustrate possible organizational intermediates in the evolution of the acoelomate from the eucoelomate condition in annelids.     

Annelids in evolutionary developmental biology and comparative genomics

Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.     

Developmental genetic evidence for a monophyletic origin of the bilaterian brain

The widely held notion of an independent evolutionary origin of invertebrate and vertebrate brains is based on classical phylogenetic, neuroanatomical and embryological data. The interpretation of these data in favour of a polyphyletic origin of animals brains is currently being challenged by three fundamental findings that derive from comparative molecular, genetic and developmental analyses. First, modern molecular systematics indicates that none of the extant animals correspond to evolutionary intermediates between the protostomes and the deuterostomes, thus making it impossible to deduce the morphological organization of the ancestral bilaterian or its brain from living species. Second, recent molecular genetic evidence for the body axis inversion hypothesis now supports the idea that the basic body plan of vertebrates and invertebrates is similar but inverted, suggesting that the ventral nerve chord of protostome invertebrates is homologous to the dorsal nerve cord of deuterostome chordates. Third, a developmental genetic analysis of the molecular control elements involved in early embryonic brain patterning is uncovering the existence of structurally and functionally homologous genes that have comparable and interchangeable functions in key aspects of brain development in invertebrate and vertebrate model systems. All three of these findings are compatible with the hypothesis of a monophyletic origin of the bilaterian brain. Here we review these findings and consider their significance and implications for current thinking on the evolutionary origin of bilaterian brains. We also preview the impact of comparative functional genomic analyses on our understanding of brain evolution.     

Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria

To elucidate the evolutionary origin of nervous system centralization, we investigated the molecular architecture of the trunk nervous system in the annelid Platynereis dumerilii. Annelids belong to Bilateria, an evolutionary lineage of bilateral animals that also includes vertebrates and insects. Comparing nervous system development in annelids to that of other bilaterians could provide valuable information about the common ancestor of all Bilateria. We find that the Platynereis neuroectoderm is subdivided into longitudinal progenitor domains by partially overlapping expression regions of nk and pax genes. These domains match corresponding domains in the vertebrate neural tube and give rise to conserved neural cell types. As in vertebrates, neural patterning genes are sensitive to Bmp signaling. Our data indicate that this mediolateral architecture was present in the last common bilaterian ancestor and thus support a common origin of nervous system centralization in Bilateria.     

Trochophora larvae: cell-lineages, ciliary bands, and body regions. 1. Annelida and Mollusca

The trochophora concept and the literature on cleavage patterns and differentiation of ectodermal structures in annelids ("polychaetes") and molluscs are reviewed. The early development shows some variation within both phyla, and the cephalopods have a highly modified development. Nevertheless, there are conspicuous similarities between the early development of the two phyla, related to the highly conserved spiral cleavage pattern. Apical and cerebral ganglia have almost identical origin in the two phyla, and the cell-lineage of the prototroch is identical, except for minor variations between species. The cell-lineage of the metatrochs is almost unknown, but the telotroch of annelids and the "telotroch" of the gastropod Patella originate from the 2d-cell, as does the gastrotroch in the few species which have been studied. The segmented annelid body, i.e. the region behind the peristome, develops through addition of new ectoderm from a ring of 2d-cells just in front of the telotroch. This whole region is thus derived from 2d-cells. Conversely, the mollusc body is covered by descendants of cells from both the C and D quadrants and a growth zone is not apparent. This supports the notion that the molluscs are not segmented like the annelids, and that the repeated structures seen in polyplacophorans and monoplacophorans do not represent a segmentation homologous to that of the annelids.     

Evolutionary aspects of pattern formation during clitellate muscle development

As a taxon of the lophotrochozoans, annelids have re-entered scientific investigations focusing on plesiomorphic bilaterian features and the evolutionary changes therein. The view of a clitellate-like plesiomorphic muscle arrangement in annelids has been challenged by recent investigations of polychaete muscle organization. However, there are few investigations of muscle formation in clitellate species that address this problem. Direct comparison of potential homologous muscles between these annelid groups is thus hampered. Somatic muscle formation during embryogenesis of two clitellates-the oligochaete Limnodrilus sp. and the hirudinean Erpobdella octoculata-occurs by distinct processes in each species, even though they share a closed outer layer of circular and an inner layer of longitudinal muscles characteristic of clitellates. In E. octoculata, the first emerging longitudinal muscles are distributed irregularly on the body surface of the embryo whereas the circular muscles appear in an orderly repetitive pattern along the anterioposterior axis. Both primary muscle types consist of fiber-bundles that branch at both their ends. This way the circular muscle bundles divide into a fine muscle-grid. The primary longitudinal muscles are incorporated into a second type of longitudinal muscles, the latter starting to differentiate adjacent to the ventral nerve cord. Those secondary muscles emerge in a ventral to dorsal manner, enclosing the embryo of E. octoculata. In Limnodrilus sp., one dorsal and one ventral bilateral pair of primary longitudinal muscles are established initially, elongating toward posterior. Initial circular muscles are emerging in a segmental pattern. Both muscle layers are completed later in development by the addition of secondary longitudinal and circular muscles. Some features of embryonic longitudinal muscle patterns in Limnodrilus sp. are comparable to structures found in adult polychaete muscle systems. Our findings show that comparative studies of body-wall muscle formation during clitellate embryogenesis are a promising approach to gain further information on annelid muscle arrangements.     

MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record

Both the monophyly and inter-relationships of the major annelid groups have remained uncertain, despite intensive research on both morphology and molecular sequences. Morphological cladistic analyses indicate that Annelida is monophyletic and consists of two monophyletic groups, the clitellates and polychaetes, whereas molecular phylogenetic analyses suggest that polychaetes are paraphyletic and that sipunculans are crown-group annelids. Both the monophyly of polychaetes and the placement of sipunculans within annelids are in conflict with the annelid fossil record—the former because Cambrian stem taxa are similar to modern polychaetes in possessing biramous parapodia, suggesting that clitellates are derived from polychaetes; the latter because although fossil sipunculans are known from the Early Cambrian, crown-group annelids do not appear until the latest Cambrian. Here we apply a different data source, the presence versus absence of specific microRNAs—genes that encode approximately 22 nucleotide non-coding regulatory RNAs—to the problem of annelid phylogenetics. We show that annelids are monophyletic with respect to sipunculans, and polychaetes are paraphyletic with respect to the clitellate Lumbricus, conclusions that are consistent with the fossil record. Further, sipunculans resolve as the sister group of the annelids, rooting the annelid tree, and revealing the polarity of the morphological change within this diverse lineage of animals.     

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

SUMMARY Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.