Phylogenetic distribution of microRNAs supports the basal position of acoel flatworms and the polyphyly of Platyhelminthes

Phylogenetic analyses based on gene sequences suggest that acoel flatworms are not members of the phylum Platyhelminthes, but instead are the most basal branch of triploblastic bilaterians. Nonetheless, this result has been called into question. An alternative test is to use qualitative molecular markers that should, in principle, exclude the possibility of convergent (homoplastic) evolution in unrelated groups. microRNAs (miRNAs), noncoding regulatory RNA molecules that are under intense stabilizing selection, are a newly discovered set of phylogenetic markers that can resolve such taxonomic disputes. The acoel Childia sp. has recently been shown to possess a subset of the conserved core of miRNAs found across deuterostomes and protostomes, whereas a polyclad flatworm-in addition to this core subset-possesses miRNAs restricted to just protostomes. Here, we examine another acoel, Symsagittifera roscoffensis, and three other platyhelminths. Our results show that the distribution of miRNAs in S. roscoffensis parallels that of Childia. In addition, two of 13 new miRNAs cloned from a triclad flatworm are also found in other lophotrochozoan protostomes, but not in ecdysozoans, deuterostomes, or in basal metazoans including acoels. The limited set of miRNAs found in acoels, intermediate between the even more reduced set in cnidarians and the larger and expanding set in the rest of bilaterians, is compelling evidence for the basal position of acoel flatworms and the polyphyly of Platyhelminthes.     

The Hox gene complement of acoel flatworms, a basal bilaterian clade

Several molecular data sets suggest that acoelomorph flatworms are not members of the phylum Platyhelminthes but form a separate branch of the Metazoa that diverged from all other bilaterian animals before the separation of protostomes and deuterostomes. Here we examine the Hox gene complement of the acoel flatworms. In two distantly related acoel taxa, we identify only three distinct classes of Hox gene: an anterior gene, a posterior gene, and a central class gene most similar to genes of Hox classes 4 and 5 in other Bilateria. Phylogenetic analysis of these genes, together with the acoel caudal homologue, supports the basal position of the acoels. The similar gene sets found in two distantly related acoels suggest that this reduced gene complement may be ancestral in the acoels and that the acoels may have diverged from other bilaterians before elaboration of the 8- to 10-gene Hox cluster that characterizes most bilaterians.     

Lipid biosynthesis in the marine flatworm Convoluta roscoffensis and its algal symbiont Platymonas convoluta.

As a part of an investigations on the lipid metabolism in Platyhelminthes, the acoel Convoluta roscoffensis, which harbors the green alga Platymonas convoluta as a symbiont, was studied. Isotopic tracer experiments established that the acoel lacks the ability to synthesize de novo long-chain saturated and unsaturated fatty acids and depends on its algal symbiont for these compounds. The acoel's fatty acid composition closely resembles that of the alga but differs from those of other animals; the acoel's polyunsaturated fatty acids are of the plant type (omega 3 family) rather than of the animal type (omega 6 family). The acoel also lacks the ability to synthesize sterols de novo. It contains 24-methylenecholesterol synthesized by the algae and, in addition, significant amounts of cholesterol, which is probably a host modification product of the algal sterol. With fatty acids provided by the symbiont, the acoel has the ability to synthesize its own complex lipids. The acoel contains relatively large amounts of triglyceride, phosphatidylcholine, and ethanolamine plasmalogen. These compounds are either not present at all or present only in minute amounts in the symbiotic alga. Since acoels belong to the most primitive forms of the present-day flatworms, the observed metabolic defects in this organism suggest that mechanisms for the biosynthesis of fatty acids and sterols were lost early during the evolution of the Platyhelminthes, and that this phenomenon is widespread within the phylum.     

To Be or Not to Be a Flatworm: The Acoel Controversy

Since first described, acoels were considered members of the flatworms (Platyhelminthes). However, no clear synapomorphies among the three large flatworm taxa - the Catenulida, the Acoelomorpha and the Rhabditophora - have been characterized to date. Molecular phylogenies, on the other hand, commonly positioned acoels separate from other flatworms. Accordingly, our own multi-locus phylogenetic analysis using 43 genes and 23 animal species places the acoel flatworm Isodiametra pulchra at the base of all Bilateria, distant from other flatworms. By contrast, novel data on the distribution and proliferation of stem cells and the specific mode of epidermal replacement constitute a strong synapomorphy for the Acoela plus the major group of flatworms, the Rhabditophora. The expression of a piwi-like gene not only in gonadal, but also in adult somatic stem cells is another unique feature among bilaterians. These two independent stem-cell-related characters put the Acoela into the Platyhelminthes-Lophotrochozoa clade and account for the most parsimonious evolutionary explanation of epidermal cell renewal in the Bilateria. Most available multigene analyses produce conflicting results regarding the position of the acoels in the tree of life. Given these phylogenomic conflicts and the contradiction of developmental and morphological data with phylogenomic results, the monophyly of the phylum Platyhelminthes and the position of the Acoela remain unresolved. By these data, both the inclusion of Acoela within Platyhelminthes, and their separation from flatworms as basal bilaterians are well-supported alternatives.     

Elongation factor 1-alpha sequences do not support an early divergence of the Acoela

The phylogenetic position of the Acoela is a key problem in the understanding of metazoan evolution. Recent studies based on 18S ribosomal DNA (rDNA) sequences have placed the Acoela in an extremely basal position as the sister group to all other extant triploblastic animals, suggesting that the phylum Platyhelminthes is polyphyletic. In order to test the results obtained with 18S rDNA, we sequenced elongation factor 1-alpha (EF1a) for the acoel Convoluta roscoffensis and five species of Turbellaria (two polyclads, Leptoplana tremellaris, and Prostheceraeus vittatus, and three triclads, Crenobia alpina, Schmidtea polychroa, and Girardia tigrina). Phylogenetic analyses of EF1a sequences show that the acoel sequences branch within the Platyhelminthes, in opposition to the 18S rDNA data. Moreover, comparison of the central variable region of EF1a shows similar sequence signatures between C. roscoffensis and the three triclad species. Although EF1a sequences fail to prove the monophyly of the phylum Platyhelminthes, they do not confirm the early divergence of the Acoela.     

Hox and ParaHox Genes in Flatworms: Characterization and Expression

Flatworms (phylum Platyhelminthes) are favourite organisms inDevelopmental Biology and Zoology because of their extraordinarypowers of regeneration and because they may hold a pivotal placein the origin and evolution of the Bilateria. Hox genes playkey roles in both processes: setting up the new anteroposteriorpattern in the former, and as qualitative markers of phylogeneticaffinities among bilaterian phyla in the latter. We have searchedfor Hox and ParaHox genes in several flatworm groups spanningfrom freshwater triclads to marine polyclads and, more recently,in the acoels, the likely earliest extant bilaterian. We haveisolated and sequenced eight Hox genes from the freshwater tricladGirardia tigrina and three Hox and two ParaHox genes from thepolyclad Discocelis tigrina. Data from the acoels Paratomellarubra and Convoluta roscoffensis is also reported. FlatwormHox sequences and 18S rDNA sequence data support clear affinitiesof Platyhelminthes to spiralian lophotrochozoans. The basalposition of acoel flatworms supported from recent 18S rDNA data,remains still uncertain. Expression of Hox genes in intact andregenerating adult organisms show nested patterns with gradedanterior expression boundaries, or ubiquitous expression. Newapproaches to study the function of Hox genes in flatworms,such as RNA interference are briefly discussed.     

The Homology of Cortical Microtubules in Platyhelminth Spermatozoa: a Comparative Immunocytochemical Study of Acetylated Tubulin

Spermatozoa of certain acoels, a group of primitive Platyhelminthes, and spermatozoa of the most derived Platyhelminthes, the Cercomeridea (parasitic Platyhelminthes), show a general morphological resemblance in that they are long filiform cells with two incorporated axonemes and longitudinal cortical microtubules. A possible way to test the homology of these cortical microtubules in the different groups is to analyze the presence/absence of post-translational modifications of tubulin. An indirect immunofluorescence study showed that the doublet microtubules of the sperm axonemes are labelled by an anti acetylated-alpha-tubulin antibody in all groups, irrespective of the axoneme pattern (9 + 0, 9 + 2 and non-trepaxonematan 9 + “1” in various acoels, and trepaxonematan 9 + “1” of the temnocephalid Troglocaridicola sp., the digenean Echinostoma caproni and the monopisthocotylean monogenean Pseudodactylogyrus sp.). Significant differences are found in the sperm cortical microtubules: they are acetylated in the acoel Actinoposthia beklemischevi, but not in the digenean E. caproni and the temnocephalid Troglocaridicola sp. These results suggest that the sperm cortical microtubules of the acoels are not homologous with the morphologically similar elements found in the higher Platyhelminthes.     

Ultrastructure and tubulin immunocytochemistry of the copulatory stylet-like structure in Childia species (Acoela)

One of the main characters used in acoel taxonomy is the male copulatory organ. Despite this, ultrastructural studies of this structure are scarce. We studied the ultrastructure of the copulatory organ in eight species of acoels belonging to the taxon Childia. Members of Childia possess a well-developed conical or cylindrical stylet-like structure composed of needles. Immunogold cytochemistry of tubulin was used to determine the composition of the needles. Stylet-like structures of Childia species at the ultrastructural level are basically similar. Stylet needles show intracellular differentiations. As shown both by ultrastructural and immunocytochemical methods, the stylet needles, in all species studied, are composed of long, parallel microtubules, either tightly packed or polymerized. We report unusual polymerization of microtubules, resulting in formation of a honeycomb-like structure in cross section. Variations of ultrastructure among Childia species include numbers and arrangement of stylet needles, shape of needles, needle compactness, microtubule polymerization, direction of stylet growth, and presence/absence of different types of granules. The stylet-like structures are homologous within Childia, but are likely to prove nonhomologous with the other needle-like structures found in acoel copulatory organs. Stylets in Platyhelminthes are not homologous with stylet-like structures in acoels.     

Mitochondrial genome data support the basal position of Acoelomorpha and the polyphyly of the Platyhelminthes

We determined 9.7, 5.2, and 6.8 kb, respectively, of the mitochondrial genomes of the acoel Paratomella rubra, the nemertodermatid Nemertoderma westbladi, and the free-living rhabditophoran platyhelminth Microstomum lineare. The identified gene arrangements are unique among metazoans, including each other, sharing no more than one or two single gene boundaries with a few distantly related taxa. Phylogenetic analysis of the amino acid sequences inferred from the sequenced genes confirms that the acoelomorph flatworms (acoels+nemertodermatids) do not belong to the Platyhelminthes, but are, instead, the most basal extant bilaterian group. Therefore, the Platyhelminthes, as traditionally constituted, is a polyphyletic phylum.     

Structure and evolution of the pharynx simplex in acoel flatworms (Acoela)

The homology of pharynges within the mostly pharynx‐less Acoela has been a matter of discussion for decades and even the basic question of whether a pharynx is a primitive trait within the Acoela and homologous to the pharynx of platyhelminth turbellarians is open. By using fluorescence staining of musculature, as well as conventional histological techniques and transmission electron microscopy, the present study sets focus on the mouth and pharynx (where present) of seven species of Acoela within Paratomellidae, Solenofilomorphidae, Hofsteniidae, Proporidae, and Convolutidae, as well as one species of Nemertodermatida and Catenulida, respectively. It is shown that among the investigated families of acoels there is a great variability in muscle systems associated with the mouth and pharynx and that pharynx histology and ultrastructural characters are widely diverse. There are no close similarities between the acoel pharynges and the catenulid pharynx but there is a general resemblance of the musculature associated with the mouth in the representatives of Paratomellidae and Nemertodermatida. On the basis of the profound differences in pharynx morphology, three major conclusions are drawn: 1) the pharynges as present in Recent acoels are not homologous to the pharynx simplex characteristic for Catenulida and Macrostomida within the Platyhelminthes; 2) the different muscular pharynx types of acoels are not homologous between higher taxa and thus a single acoel‐type pharynx simplex cannot be defined; 3) the presence of a muscular pharynx most likely does not represent the ancestral state. J. Morphol, 2009. © 2008 Wiley‐Liss, Inc.     

Expression of the 22 nucleotide let‐7 heterochronic RNA throughout the Metazoa: a role in life history evolution?

The 22 nucleotide let-7 small temporal RNA has been found consistently in samples from diverse bilateria but not from sponge or cnidarians. Here we further examine the phylogenetic distribution of this regulatory RNA by sampling representatives of diverse metazoan lineages. The 22 nucleotide let-7 RNA is detectable in triclad and polyclad platyhelminths, nemertean, and chaetognath but not ctenophore or acoel metazoans. These results support recent arguments that acoels are distinct from other acoelomate platyhelminths. We argue that let-7 is not a bilaterian or triploblast synapomorphy but instead evolved later in metazoan evolution, perhaps in association with complex life history traits.     

Patterns of musculature as taxonomic characters for the Turbellaria Acoela

While turbellarians are generally assumed to have body-wall musculature consisting routinely of longitudinal, circular, and diagonal fibers, members of the Acoela examined by a fluorescence-microscopy technique specific for actin showed more complicated and distinctive arrangements of muscles, giving promise for better delimiting taxa within this taxonomically difficult order. Certain globose or tear-drop-shaped worms such as Convoluta pulchra and species of Pseudaphanostoma, Mecynostomum, and Otocelis, showed a complex pattern in which muscles longitudinal in the anterior half of the body arc diagonally across the posterior half; complex brushes of parenchymal muscles that cross at the level of the statocyst and arc postero-laterally also characterize these groups. The more elongate acoel Paratomella sp. was found to have musculature dominated by strictly longitudinal fibers and with relatively weak circular fibers and few fibers running diagonally to the body axis, yet the elongate mecynostomid Paedomecynostomum bruneum showed a crossing of antero-longitudinal fibers similar to that seen in the more globose Mecynostomum sp. A distinctive looping of muscles around the mouth is seen in P. bruneum and the Anaperidae. Such similarities and differences in pattern of musculature promise to provide easily recognizable characters for taxonomy of the Acoela at levels ranging from species to family. This revised version was published online in July 2006 with corrections to the Cover Date.     

How the worm got its pharynx: phylogeny, classification and Bayesian assessment of character evolution in Acoela

Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.     

Are the Platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences

In most zoological textbooks, Platyhelminthes are depicted as an early- emerging clade forming the likely sister group of all the other Bilateria. Other phylogenetic proposals see them either as the sister group of most of the Protostomia or as a group derived from protostome coelomate ancestors by progenesis. The main difficulty in their correct phylogenetic placing is the lack of convincing synapomorphies for all Platyhelminthes, which may indicate that they are polyphyletic. Moreover, their internal phylogenetic relationships are still uncertain. To test these hypotheses, new complete 18S rDNA sequences from 13 species of "Turbellaria" have been obtained and compared to published sequences of 2 other "Turbellaria," 3 species of parasitic Platyhelminthes, and several diploblastic and deuterostome and protostome triploblastics. Maximum-parsimony, maximum-likelihood, and neighbor-joining methods were used to infer their phylogeny. The results show the order Catenulida to form an independent early- branching clade and emerge as a potential sister group of the rest of the Bilateria, while the rest of Platyhelminthes (Rhabditophora), which includes the parasites, form a clear monophyletic group closely related to the protostomes. The order Acoela, morphologically considered as candidates to be ancestral, are shown to be fast-clock organisms for the 18S rDNA gene. Hence, long-branching of acoels and insufficient sampling of catenulids and acoels leave their position still unresolved and call for further studies. Within the Rhabditophora, our analyses suggest (1) a close relationship between orders Macrostomida and Polycladida, forming a clear sister group to the rest of orders; (2) that parasitic platyhelminthes appeared early in the evolution of the group and form a sister group to a still-unresolved clade made by Nemertodermatida, Lecithoepitheliata, Prolecithophora, Proseriata, Tricladida, and Rhabdocoela; and (3) that Seriata is paraphyletic.      

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.     

Molecular systematics of the Acoela (Acoelomorpha,Platyhelminthes) and its concordance with morphology

The phylogenetic relationships of the lower worm group Acoela were investigated using newly obtained nuclear 18S rDNA sequences from 16 acoels in combination with 16 acoel sequences available on GenBank from other laboratories. Parsimony and maximum likelihood analyses of the molecular data supported the concept that the Acoela is monophyletic; however, the gene tree produced by these analyses conflicts with the current taxonomic system for the Acoela in several family-level groupings. Most notable is the apparent polyphyly of the largest family of acoels, the Convolutidae. DNA analysis grouped together species of small-bodied convolutids in one clade, while large-bodied convolutids grouped in a separate clade with other large-bodied acoels. Despite such conflicts, the branching pattern in the gene tree is well supported by morphological characters of sperm and body-wall musculature.     

Evolution of body-wall musculature in the Platyhelminthes (Acoelomorpha, Catenulida, Rhabditophora)

In an effort to understand the phylogeny of the Platyhelminthes, the patterns of body-wall musculature of flatworms were studied using fluorescence microscopy and Alexa-488-labeled phalloidin. Species of the Catenulida have a simple orthogonal gridwork of longitudinal and circular muscles. Members of the Rhabditophora have the same gridwork of musculature, but also have diagonal muscles over their entire body. Although a few species of Acoelomorpha possessed a simple orthogonal grid of musculature, most species typically have distinctly different patterns of dorsal and ventral body-wall musculature that include sets of longitudinal, circular, U-shaped, and several kinds of diagonal muscles. Several distinct patterns of musculature were identified, including 8 patterns in 11 families of acoels. These patterns have proven to be useful in clarifying the phylogeny of the Acoelomorpha, particularly with regard to the higher acoels. Patterns of musculature as well as other morphological characters are used here for revisions of acoel systematics, including the return of Eumecynostomum sanguineum (Mecynostomidae) to the genus Aphanostoma (Convolutidae), the revision of the family Childiidae, and the formation of a new family, Actinoposthiidae.     

Ultrastructure of sperms in Acoela (Acoelomorpha) and its concordance with molecular systematics

Abstract. The sperms of the Acoela, a group of lower worms, are filiform cells with 2 flagella incorporated into the cell body. Their axonemes can variously have 9+2, 9+1, or 9+0 patterns of microtubules; and singlet microtubules in the cell body can be arranged in axial or cortical positions. An analysis of phylogenetic relationships of acoels based on molecular characters (18S rDNA sequence data) showed that these patterns of microtubules, where known, fell into discrete monophyletic groups. To test this hypothesis, we have expanded the database of sperm characters by examining the ultrastructure of a further 10 species representing 4 acoel families. As expected, the Convolutidae fell into 2 unrelated groups: “small‐bodied convolutids”(Convoluta pulchra, Praeconvoluta tigrina, Pseudaphanostoma smithrii) having 9+2 axonemes and cortical microtubules, and “large‐bodied convolutids” (including Wulguru cuspidata) having 9+0 axonemes and axial microtubules. Also, as expected, a member of the Mecynostomidae (Paedomecynostomum bruneum) has 9+1 axonemes and axial microtubules. Members of a family that appears intermediate by molecular characters, the Otocelididae, significantly have a variety of patterns: axonemes with both 9+2 and 9+0 patterns (Notocelis gullmarensis) or just 9+2 (the other species), and either axial (Philocelis brueggemanni), both axial and cortical (N. gullmarensis) microtubules, or microtubules that bend between axial and cortical positions along the length of the sperm (Otocelis sandara). Members of the Dakuidae (Daku woorimensis) also belong to this intermediate group, having 9+2 axonemes and axial microtubules, while in a fifth otocelidid (Stomatricha hochbergi), sperm characters are like those of the “large‐bodied convolutids” (9+0 axonemes and axial microtubules). Characters of sperm morphology generally support the molecular hypothesis of relationships and confirm a suspected polyphyly of the families Convolutidae, Otocelididae, and Actinoposthiidae.     

Hidden diversity of Acoelomorpha revealed through metabarcoding

Animals with bilateral symmetry comprise the majority of the described species within Metazoa. However, the nature of the first bilaterian animal remains unknown. As most recent molecular phylogenies point to Xenacoelomorpha as the sister group to the rest of Bilateria, understanding their biology, ecology and diversity is key to reconstructing the nature of the last common bilaterian ancestor (Urbilateria). To date, sampling efforts have focused mainly on coastal areas, leaving potential gaps in our understanding of the full diversity of xenacoelomorphs. We therefore analysed 18S rDNA metabarcoding data from three marine projects covering benthic and pelagic habitats worldwide. Our results show that acoels have a greater richness in planktonic environments than previously described. Interestingly, we also identified a putative novel clade of acoels in the deep benthos that branches as sister group to the rest of Acoela, thus representing the earliest-branching acoel clade. Our data highlight deep-sea environments as an ideal habitat to sample acoels with key phylogenetic positions, which might be useful for reconstructing the early evolution of Bilateria.