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

Phylogenetic assessment and systematic revision of the acoel family Isodiametridae

Isodiametridae is a large family of Acoela with 22 nominal genera and nearly 100 species. Unfortunately, systematics of Isodiametridae, as it stands, is highly problematic. Genera frequently have been proposed without reference to an explicit phylogenetic hypothesis, such that the current classification system holds little or no predictive power. Many taxa do not fit with the family diagnosis, and it is increasingly difficult to determine in which taxon a new species should be described. Herein, we reconstruct the phylogenetic relationships of Acoela with a focus on Isodiametridae using both previously published and new ribosomal and mitochondrial sequence data. Our dataset comprises sequences from 45 species representing 16 of the 22 isodiametrid genera. Our results recovered a well-supported Isodiametridae, but provided further evidence that the family and several genera within require revision. We have updated the classification system of Isodiametridae to be consistent with its phylogeny, including the transference of Otocelis to Otocelididae, Postaphanostoma and Faerlea to Mecynostomidae and Alluna to Actinoposthiidae. Six other genera are placed in synonymy. We review the morphological taxonomy and provide an identification key of the genera in the revised family.

Phylogeny and highland adaptation of Chinese species in Allium section Daghestanica (Amaryllidaceae) revealed by transcriptome sequencing

Allium L. is one of the largest monocotyledonous genera with extensive distribution in the Northern Hemisphere. The fundamental phylogenies of Allium have been investigated using many morphological and molecular characters. However, the morphological characters may not agree with the molecular results in some Allium groups or sections (such as the Chinese Allium section Daghestanica), which may result in ambiguous species relationships and hinder further evolutionary and adaptive researches. Here, transcriptome sequences of the six Chinese endemics from Allium section Daghestanica were collected, with their single-copy genes (SCGs) were extracted. The interspecies relationships were analyzed using concatenation and coalescent methods. The branch-site model (BSM) was conducted to detect the positively selected genes (PSGs) in five highland species of this section. Based on 1644, 1281 and 1580 SCGs in flowers, leaves, and flowers-leaves combination respectively, a robust consistent and well-resolved phylogeny was generated from the concatenation method. Strong conflicts among individual gene trees were detected in the coalescent method, and morphological characters were incongruent with molecular relationships to some degree. Many PSGs were involved in responses of various stresses and stimuli (e.g. hypoxia, low temperature, aridity), DNA repair, metabolism, nutrient or energy intake, photosynthesis, and signal transduction. Our study revealed a clear interspecies relationship of Chinese endemics in Allium section Daghestanica and suggested that the discordance between morphological characters and molecular relationships might result from that the former are more susceptible to convergence compared with the latter. PSGs detected in our study may provide some insights into highland adaptation in Allium species.

Acoel regeneration mechanisms indicate an ancient role for muscle in regenerative patterning

Positional information is required for animal regeneration, yet how it is harbored in adult tissues is poorly understood. In planarians, positional control genes (PCGs) control regeneration outcomes and are regionally expressed predominately in the musculature. Acoels are early diverging bilaterally symmetric animals, having separated from other bilaterians > 550 million years ago. Here, we find that PCGs in the acoel Hofstenia miamia are expressed together and specifically in a primary differentiated cell type: muscle. The vast majority of Hofstenia muscle cells in regions tested express PCGs, suggesting positional information is a major feature of muscle. PCG expression domains are dynamic in muscle after injury, consistent with known PCG roles in guiding regeneration. These data demonstrate an instructive positional role for Hofstenia muscle and this similarity with planarians suggests mesodermal muscle originated at the base of the Bilateria not only for contraction, but also as the source of positional information guiding regeneration.

Mesodermal gene expression in the acoel Isodiametra pulchra indicates a low number of mesodermal cell types and the endomesodermal origin of the gonads

Acoelomorphs are bilaterally symmetric small marine worms that lack a coelom and possess a digestive system with a single opening. Two alternative phylogenetic positions of this group within the animal tree are currently debated. In one view, Acoelomorpha is the sister group to all remaining Bilateria and as such, is a morphologically simple stepping stone in bilaterian evolution. In the other, the group is a lineage within the Deuterostomia, and therefore, has derived a simple morphology from a more complex ancestor. Acoels and the closely related Nemertodermatida and Xenoturbellida, which together form the Acoelomorpha, possess a very limited number of cell types. To further investigate the diversity and origin of mesodermal cell types we describe the expression pattern of 12 orthologs of bilaterian mesodermal markers including Six1/2, Twist, FoxC, GATA4/5/6, in the acoel Isodiametra pulchra. All the genes are expressed in stem cells (neoblasts), gonads, and at least subsets of the acoel musculature. Most are expressed in endomesodermal compartments of I. pulchra developing embryos similar to what has been described in cnidarians. Our molecular evidence indicates a very limited number of mesodermal cell types and suggests an endomesodermal origin of the gonads and the stem cell system. We discuss our results in light of the two prevailing phylogenetic positions of Acoelomorpha.

The Acoela: on their kind and kinships, especially with nemertodermatids and xenoturbellids (Bilateria incertae sedis)

Acoels are among the simplest worms and therefore have often been pivotal in discussions of the origin of the Bilateria. Initially thought primitive because of their “planula-like” morphology, including their lumenless digestive system, they were subsequently dismissed by many morphologists as a specialized clade of the Platyhelminthes. However, since molecular phylogenies placed them outside the Platyhelminthes and outside all other phyla at the base of the Bilateria, they became the focus of renewed debate and research. We review what is currently known of acoels, including information regarding their morphology, development, systematics, and phylogenetic relationships, and put some of these topics in a historical perspective to show how the application of new methods contributed to the progress in understanding these animals. Taking all available data into consideration, clear-cut conclusions cannot be made; however, in our view it becomes successively clearer that acoelomorphs are a “basal” but “divergent” branch of the Bilateria.

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.

Steps towards a centralized nervous system in basal bilaterians: insights from neurogenesis of the acoel Symsagittifera roscoffensis

Due to its proposed basal position in the bilaterian Tree of Life, Acoela may hold the key to our understanding of the evolution of a number of bodyplan features including the central nervous system. In order to contribute novel data to this discussion we investigated the distribution of α-tubulin and the neurotransmitters serotonin and RFamide in juveniles and adults of the sagittiferid Symsagittifera roscoffensis. In addition, we present the expression pattern of the neuropatterning gene SoxB1. Adults and juveniles exhibit six serotonergic longitudinal neurite bundles and an anterior concentration of serotonergic sensory cells. While juveniles show an "orthogon-like" arrangement of longitudinal neurite bundles along the anterior-posterior axis, it appears more diffuse in the posterior region of adults. Commissures between the six neurite bundles are present only in the anterior body region of adults, while irregularly distributed individual neurites, often interconnected by serotonergic nerve cells, are found in the posterior region. Anti-RFamide staining shows numerous individual neurites around the statocyst. The orthogon-like nervous system of S. roscoffensis is confirmed by α-tubulin immunoreactivity. In the region of highest neurotransmitter density (i.e., anterior), the HMG-box gene SrSoxB1, a transcription factor known to be involved in neurogenesis in other bilaterians, is expressed in juvenile specimens. Accordingly, SoxB1 expression in S. roscoffensis follows the typical pattern of higher bilaterians that have a brain. Thus, our data support the notion that Urbilateria already had the genetic toolkit required to form brain-like neural structures, but that its morphological degree of neural concentration was still low.

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.

Myogenesis in the basal bilaterian Symsagittifera roscoffensis (Acoela)

BACKGROUND

In order to increase the weak database concerning the organogenesis of Acoela - a clade regarded by many as the earliest extant offshoot of Bilateria and thus of particular interest for studies concerning the evolution of animal bodyplans - we analyzed the development of the musculature of Symsagittifera roscoffensis using F-actin labelling, confocal laserscanning microscopy, and 3D reconstruction software.

RESULTS

At 40% of development between egg deposition and hatching short subepidermal fibres form. Muscle fibre development in the anterior body half precedes myogenesis in the posterior half. At 42% of development a grid of outer circular and inner longitudinal muscles is present in the bodywall. New circular muscles either branch off from present fibres or form adjacent to existing ones. The number of circular muscles is higher than that of the longitudinal muscles throughout all life cycle stages. Diagonal, circular and longitudinal muscles are initially rare but their number increases with time. The ventral side bears U-shaped muscles around the mouth, which in addition is surrounded by a sphincter muscle. With the exception of the region of the statocyst, dorsoventral muscles are present along the entire body of juveniles and adults, while adults additionally exhibit radially oriented internal muscles in the anterior tip. Outer diagonal muscles are present at the dorsal anterior tip of the adult. In adult animals, the male gonopore with its associated sexual organs expresses distinct muscles. No specific statocyst muscles were found. The muscle mantles of the needle-shaped sagittocysts are situated along the lateral edges of the animal and in the posterior end close to the male gonopore. In both juveniles and adults, non-muscular filaments, which stain positively for F-actin, are associated with certain sensory cells outside the bodywall musculature.

CONCLUSION

Compared to the myoanatomy of other acoel taxa, Symsagittifera roscoffensis shows a very complex musculature. Although data on presumably basal acoel clades are still scarce, the information currently available suggests an elaborated musculature with longitudinal, circular and U-shaped muscles as being part of the ancestral acoel bodyplan, thus increasing the possibility that Urbilateria likewise had a relatively complicated muscular ground pattern.

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.

Copulatory organ musculature in Childia (Acoela) as revealed by phalloidin fluorescence and confocal microscopy

Copulatory organs of eight species of the monophyletic taxon Childia were investigated in detail, using phalloidin fluorescence method and confocal microscopy. Childia species were shown to have one, two or several tubular stylets, conical to cylindrical in shape, composed of few to numerous needles. The musculature varied greatly, from the absence of seminal vesicle to extensively developed seminal vesicles with several additional types of specialized muscles. Ten copulatory organ characters were coded and mapped on the total evidence tree. The data obtained permitted to follow the evolution of the Childia stylet and to demonstrate that the structure of the stylet apparatus is largely consistent with the phylogeny of the group (CI=0.75). Possible function of different muscle specializations was discussed.

Comparative morphology of the bursal nozzles in acoels (Acoela, Acoelomorpha)

Systematics of the Acoela is particularly difficult because of the paucity of readily discernible morphological features. In other soft-bodied worms, sclerotized structures, such as copulatory stylets, provide important characters that can be seen in whole mounts, but acoels generally lack such features. Among the few sclerotized structures in acoels are bursal nozzles-tubiform outlets on the seminal bursae that are believed to be conduits (spermatic ducts) through which allosperm are transported to the oocytes. Early classifications of the Acoela used features of the female reproductive system, including bursal nozzles, for distinguishing major groups, but the current system essentially ignores them as too plastic to provide higher-level distinctions. We used confocal and electron microscopy to further characterize bursal nozzles in five acoel species, and found all composed of actin-reinforced extensions of stacked, flat mesenchymal cells. In Notocelis gullmarensis, Aphanostoma bruscai, and Daku woorimensis, the nozzle is a stiffened region of the same cells forming the wall of the bursa. By contrast, in Wulguru cuspidata cells forming the nozzle are distinct from those of the bursa. The so-called bursal cap of A. bruscai and D. woorimensis has small sclerotized disjunct units within it, also composed of stacked, flat, actin-reinforced cells. The nozzle of W. cuspidata, prominent like that of other convolutid acoels, is relatively complex, its actin-reinforced cells sandwiched with secretory cells and its base bearing a "sorting apparatus" of egg-shaped cells that send narrow processes inside the spermatic duct. Cases of sperm inside the nozzle corroborate its assumed role in reproduction. Whereas most nozzles sit at the end of the bursa facing the ovary, in species of Pseudmecynostomum and purportedly in a few other acoels, they sit between the female pore and the bursa, constituting what we call a vaginal nozzle. All bursal nozzles of acoels show a common ground pattern indicating common ancestry, but certain features discerned through electron and confocal microscopy show promise of providing synapomorphies for grouping some species.

Systematics of Chaetognatha under the light of molecular data, using duplicated ribosomal 18S DNA sequences

While the phylogenetic position of Chaetognatha has became central to the question of early bilaterian evolution, the internal systematics of the phylum are still not clear. The phylogenetic relationships of the chaetognaths were investigated using newly obtained small subunit ribosomal RNA nuclear 18S (SSU rRNA) sequences from 16 species together with 3 sequences available in GenBank. As previously shown with the large subunit ribosomal RNA 28S gene, two classes of Chaetognatha SSU rRNA gene can be identified, suggesting a duplication of the whole ribosomal cluster; allowing the rooting of one class of genes by another in phylogenetic analyses. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the molecular data, and statistical tests showed (1) that there are three main monophyletic groups: Sagittidae/Krohnittidae, Spadellidae/Pterosagittidae, and Eukrohniidae/Heterokrohniidae, (2) that the group of Aphragmophora without Pterosagittidae (Sagittidae/Krohnittidae) is monophyletic, (3) the Spadellidae/Pterosagittidae and Eukrohniidae/Heterokrohniidae families are very likely clustered, (4) the Krohnittidae and Pterosagittidae groups should no longer be considered as families as they are included in other groups designated as families, (5) suborder Ctenodontina is not monophyletic and the Flabellodontina should no longer be considered as a suborder, and (6) the Syngonata/Chorismogonata and the Monophragmophora/Biphragmophora hypotheses are rejected. Such conclusions are considered in the light of morphological characters, several of which are shown to be prone to homoplasy.

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.

Molecular insights into Cumacean family relationships (Crustacea, Cumacea)

Cumaceans are a diverse order of small, benthic marine crustaceans. Phylogenetic hypotheses for the eight currently recognized cumacean families have not been formally proposed. However, based on external morphological traits and Linnean classification, a few conflicting hypotheses of relatedness have been proposed. Family definitions rely on morphological characters that often overlap and diagnoses are based on a combination of non-unique characters. Morphological analysis does not provide a well-resolved phylogeny. In the present study, we use amino acid sequences from the mitochondrial cytochrome oxidase I gene to produce a molecular phylogenetic hypothesis for the families of Cumacea. Phylogenetic analyses at the amino acid level were performed under Bayesian, likelihood, and parsimony methods. Results strongly suggest that families lacking an articulated telson form a monophyletic group. This pleotelson clade, composed of the families Bodotriidae, Leuconidae, and Nannastacidae, is the most derived within the Cumacea. Within this group, the Bodotriidae resolve paraphyletically, with Leuconidae and Nannastacidae embedded within it. Comparison of the molecular phylogeny with that based on morphology suggests that many "diagnostic" characters are homoplasious.

Molecular phylogeny of the Platyhelminthes

The phylum Platyhelminthes has traditionally been considered the most basal bilaterian taxon. The main difficulty with this placement is the lack of convincing synapomorphies for all Platyhelminthes, which suggest that they are polyphyletic. Recent molecular findings based on 18S rDNA sequence data and number and type of Hox genes strongly suggest that the majority of Platyhelminthes are members of the lophotrochozoan protostomes, whereas the Acoelomorpha (Acoela + Nemertodermatida) fall outside of the Platyhelminthes as the most basal bilaterian taxon. Here we review phylum-wide analyses based on complete ribosomal and other nuclear genes addressed to answer the main issues facing systematics and phylogeny of Platyhelminthes. We present and discuss (i) new corroborative evidence for the polyphyly of the Platyhelminthes and the basal position of Acoelomorpha; (ii) a new consensus internal tree of the phylum; (iii) the nature of the sister group to the Neodermata and the hypotheses on the origin of parasitism; and (iv) the internal phylogeny of some rhabditophoran orders. Some methodological caveats are also introduced. The need to erect a new phylum, the Acoelomorpha, separate from the Platyhelminthes (now Catenulida + Rhabditophora) and based on present and new morphological and molecular characters is highlighted, and a proposal made.