Background: Xenacoelomorpha is a marine clade of microscopic worms that is an important model system for understanding the evolution of key bilaterian novelties, such as the excretory system. Nevertheless, Xenacoelomorpha genomics has been restricted to a few species that either can be cultured in the lab or are centimetres long. Thus far, no genomes are available for Nemertodermatida, one of the group's main clades and whose origin has been dated more than 400 million years ago.Methods: DNA was extracted from a single specimen and sequenced with HiFi following the PacBio Ultra-Low DNA Input protocol. After genome assembly, decontamination, and annotation, the genome quality was benchmarked using two acoel genomes and one Illumina genome as reference. The gene content of three cnidarians, three acoelomorphs, four deuterostomes, and eight protostomes was clustered in orthogroups to make inferences of gene content evolution. Finally, we focused on the genes related to the ultrafiltration excretory system to compare patterns of presence/absence and gene architecture among these clades.Results: We present the first nemertodermatid genome sequenced from a single specimen of Nemertoderma westbladi. Although genome contiguity remains challenging (N50: 60 kb), it is very complete (BUSCO: 80.2%, Metazoa; 88.6%, Eukaryota) and the quality of the annotation allows fine-detail analyses of genome evolution. Acoelomorph genomes seem to be relatively conserved in terms of the percentage of repeats, number of genes, number of exons per gene and intron size. In addition, a high fraction of genes present in both protostomes and deuterostomes are absent in Acoelomorpha. Interestingly, we show that all genes related to the excretory system are present in Xenacoelomorpha except Osr, a key element in the development of these organs and whose acquisition seems to be interconnected with the origin of the specialised excretory system.Conclusion: Overall, these analyses highlight the potential of the Ultra-Low Input DNA protocol and HiFi to generate high-quality genomes from single animals, even for relatively large genomes, making it a feasible option for sequencing challenging taxa, which will be an exciting resource for comparative genomics analyses.

Eight new species of Isodiametridae (Acoela) are presented and phylogenetic relationships of the family using 18S and COI sequence data reconstructed. Four species of Baltalimania, two species of Praeaphanostoma and two species of Pseudoposthia are described that all can be distinguished both morphologically and through differences in the DNA sequences as supported by mPTP analysis. The addition of eight new species increases the number of nominal species of Isodiametridae worldwide by 10% and within Sweden by 31%, but also highlights several taxonomic problems. Several species are now confirmed as isodiametrids that are otherwise incongruent with the family's diagnostic characters. Generic keys are presented for Baltalimania and Praeaphanostoma.

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.

Nemertodermatida is a small taxon of microscopic marine worms, which were originally classified within Platyhelminthes. Today they are hypothesized to be either an early bilaterian lineage or the sister group to Ambulacraria within Deuterostomia. These two hypotheses indicate widely diverging evolutionary histories in this largely neglected group. Here, we analyse the phylogeny of Nemertodermatida using nucleotide sequences from the ribosomal LSU and SSU genes and the protein coding Histone 3 gene. All currently known species except Ascoparia neglecta and Ascoparia secunda were included in the study in addition to several yet undescribed species. Ascopariidae and Nemertodermatidae are retrieved as separate clades, although not in all analyses as sister groups. Non-monophyly of Nemertodermatida was rejected by the Approximately Unbiased test. Nemertodermatid nucleotide sequences deposited in Genbank before 2013 were validated against our dataset; some of them are shown to be chimeric implying falsification of prior hypotheses about nemertodermatid phylogeny: other sequences should be assigned new names. We also show that the genus Nemertoderma needs revision.

Nemertodermatida are microscopic marine worms likely to be the sister group to acoels, forming with them the earliest extant branch of bilaterian animals, although their phylogenetic position is debated. The nervous system of Flagellophora cf. apelti, Sterreria spp. and Nemertoderma cf. westbladi has been investigated by immunohistochemistry and confocal microscopy using anti-tubulin, anti-5-HT and anti-FMRFamide antibodies. The nervous system of F. cf. apelti is composed of a large neuropile and a loose brain at the level of the statocysts with several nerve fibres surrounding them and innervating the broom organ. Sterreria spp. shows a commissural-like brain and several neurite bundles going frontad and caudad from this. At the level of the statocysts there is also a thicker aggregation of immunoreactive fibres. The nervous system of N. cf. westbladi consists of a nerve ring lying outside the body wall musculature at the level of the statocyst and a pair of ventro-lateral neurite bundles, from which extend thinner fibres innervating the ventral side of the animal. Numerous bottle-shaped glands were observed, innervated by fibres starting both from the brain and the neurite bundles. The nervous system of the nemertodermatids studied to date displays no common pattern; instead, there is considerable plasticity in the general morphology of the nervous system. In addition, the musculature of Sterreria spp. has been studied by phalloidin staining. It shows diagonal muscles in the anterior quarter of the body and a simple orthogonal grid in the posterior three quarters, being simpler than that of the other nemertodermatids. High-resolution differential interference contrast microscopy permitted to better visualize some morphological characters of the species studied, such as statocysts, sperm and glands and, in combination with anti-tubulin staining, describe in detail the broom organ in F. cf. apelti. Finally, we note an apparent absence of innervation of the gut in Nemertodermatida similar to the condition in Xenoturbella.

Nemertodermatida are microscopically small, benthic marine worms. Specimens of two nominal species, Sterreria psammicola and Nemertinoides elongatus from 33 locations worldwide were sequenced for three molecular markers. Species delimitation and validation was done using gene trees, haplotype networks and multilocus Bayesian analysis. We found 20 supported species of which nine: Nemertinoides glandulosum n.sp., N. wolfgangi n.sp., Sterreria boucheti n.sp., S. lundini n.sp., S. martindalei n.sp., S. monolithes n.sp., S. papuensis n.sp., S. variabilis n.sp. and S. ylvae n.sp., are described including nucleotide-based diagnoses. The distribution patterns indicate transoceanic dispersal in some of the species. Sympatric species were found in many cases. The high level of cryptic diversity in this meiofauna group implies that marine diversity may be higher than previously estimated. 

Nemertodermatida is a small taxon of marine worm-like animals; its position in the tree of life is highly contested The musculature of Nemertoderma westbladi and Meara stichopi is studied here in detail using fluorescent phalloidin and confocal microscopy.

In both species the musculature is composed of an outer layer of circular and an inner layer of longitudinal musculature, diagonal muscles form a distinct layer in N westbladi but in M. stichopi these fibres connect to both other layers. The supraterminally opening male pore and antrum are formed by invagination of the whole body-wall in both species and the seminal vesicle is lined by a thin net of musculature only in full male maturity. Modifications of the ventral body-wall adjacent to the mouth are small and transient in N. westbladi including no extra musculature whereas it consists of additional strong U-shaped musculature in M. stichopi. Myogenesis in N. westbladi is not finished in hatchlings and will be completed dorsally in juvenile specimens and ventrally in male mature ones, after the loss of the mouth.

Musculature between the two species differs considerably and might give insights into the internal relationships of Nemertodermatida and might prove to be useful in studies investigating their phylogenetic position. More data of other species and developmental changes are needed.

Gastrotricha is a cosmopolitan group of aquatic invertebrates. To date approximately 765 species have been described. This study is the first to deal with species delimitation and cryptic species of freshwater Gastrotricha. Three commonly encountered species, Heterolepidoderma ocellatum, Lepidochaetus zelinkai and Lepidodermella squamata, are investigated for cryptic speciation. Most of the material is based on Swedish specimens but closely related species from other parts of the world are also included. Taxonomic revisions are supported by phylogenies based on 18S rRNA, 28S rRNA and COI mtDNA of freshwater Chaetonotidae from several genera and inferred from Bayesian and maximum likelihood approaches. Heterolepidoderma ocellatum f. sphagnophilum is raised to species level, becoming H. acidophilum n. sp. Moreover, genetic data based on COI indicates high variation between two morphologically very similar groups of Lepidodermella squamata. The extent of cryptic speciation in L. zelinkai appears low. Based on the phylogenetic hypothesis presented in this paper the new species, Lepidodermella intermedia n. sp., from northernSweden is also described. The phylogenetic hypothesis generated show that Chaetonotidae is a non-monophyletic group.  

Background

Phylogenetic relationships within Gastrotricha are poorly known. Attempts to shed light on this subject using morphological traits have led to hypotheses lacking satisfactory statistical support; it seemed therefore that a different approach was needed.

Methodology/Principal Findings

In this paper we attempt to elucidate the relationships within the taxonomically vast family Thaumastodermatidae (Macrodasyida) using molecular sequence data. The study includes representatives of all the extant genera of the family and for the first time uses a multi-gene approach to infer evolutionary liaisons within Gastrotricha. The final data set comprises sequences of three genes (18S, 28S rDNA and COI mtDNA) from 41 species, including 29 thaumastodermatids, 11 non-thaumastodermatid macrodasyidans and a single chaetonotidan. Molecular data was analyzed as a combined set of 3 genes and as individual genes, using Bayesian and maximum likelihood approaches. Two different outgroups were used: Xenotrichula intermedia (Chaetonotida) and members of the putative basal Dactylopodola (Macrodasyida). Thaumastodermatidae and all other sampled macrodasyidan families were found monophyletic except for Cephalodasyidae. Within Thaumastodermatidae Diplodasyinae and Thaumastodermatinae are monophyletic and so are most genera. Oregodasys turns out to be the most basal group within Thaumastodermatinae in analyses of the concatenated data set as well as in analyses of the nuclear genes. Thaumastoderma appears as the sister taxon to the remaining species. Surprisingly, Tetranchyroderma is non-monophyletic in our analyses as one group of species clusters with Ptychostomella while another appears as the sister group of Pseudostomella.

Conclusions/Significance

Results in general agree with the current classification; however, a revision of the more derived thaumastodermatid taxa seems necessary. We also found that the ostensible COI sequences from several species do not conform to the general invertebrate or any other published mitochondrial genetic code; they may be mitochondrially derived nuclear genes (numts), or one or more modifications of the mitochondrial genetic code within Gastrotricha.

The freshwater gastrotrich fauna of Sweden is poorly known. Only seven species of freshwater gastrotrichs have been reported so far. This paper is the first in a series of contributions about the Swedish freshwater gastrotrich fauna. Here we describe one new species, Ichthydium skandicum n. sp., from Jamtland, northern Sweden. The new species falls within the boundary of the subgenus Forficulichthys and is morphologically closest to Ichthydium tanytrichum from which it can be differentiated based on the presence of four pairs of dorsal, keeled scales in the posterior trunk region. Moreover, we provide morphometric data for three additional Ichthydium species: I. diacanthum, I. squamigerum and I. tanytrichum, Italian species all of which are reported for the first time outside Italy. Considering the accompanying fauna, a total of thirteen freshwater Gastrotricha are reported for the first time from Sweden. Finally we present a dichotomous key for Ichthydium along with distributional data of the species considered.