Hox genes encode a family of homeodomain containing transcription factors that are clustered together on chromosomes of many Bilateria. Some bilaterian lineages express these genes during embryogenesis in spatial and/or temporal order according to their arrangement in the cluster, a phenomenon referred to as collinearity. Expression of Hox genes is well studied during embryonic and larval development of numerous species; however, relatively few studies focus on the comparison of pre- and postmetamorphic expression of Hox genes in animals with biphasic life cycle. Recently, the expression of Hox genes was described for embryos and larvae of Terebratalia transversa, a rhynchonelliformean brachiopod, which possesses distinct metamorphosis from planktonic larvae to sessile juveniles. During premetamorphic development, T. transversa does not exhibit spatial collinearity and several of its Hox genes are recruited for the morphogenesis of novel structures. In our study, we determined the expression of Hox genes in postmetamorphic juveniles of T. transversa in order to examine metamorphosis-related changes of expression patterns and to test whether Hox genes are expressed in the spatially collinear way in the postmetamorphic juveniles. Hox genes are expressed in a spatially non-collinear manner in juveniles, generally showing similar patterns as ones observed in competent larvae: genes labial and post1 are expressed in chaetae-related structures, sex combs reduced in the shell-forming epithelium, whereas lox5 and lox4 in dorso-posterior epidermis. After metamorphosis, expression of genes proboscipedia, hox3, deformed and antennapedia becomes restricted to, respectively, shell musculature, prospective hinge rudiments and pedicle musculature and epidermis. All developmental stages of T. transversa, including postmetamorphic juveniles, exhibit a spatial non-collinear Hox genes expression with only minor changes observed between pre- and postmetamorphic stages. Our results are concordant with morphological observation that metamorphosis in rhynchonelliformean brachiopods, despite being rapid, is rather gradual. The most drastic changes in Hox gene expression patterns observed during metamorphosis could be explained by the inversion of the mantle lobe, which relocates some of the more posterior larval structures into the anterior edge of the juveniles. Co-option of Hox genes for the morphogenesis of novel structures is even more pronounced in postmetamorphic brachiopods when compared to larvae.

Background: Phoronida is a small group of marine worm-like suspension feeders, which together with brachiopods and bryozoans form the clade Lophophorata. Although their development is well studied on the morphological level, data regarding gene expression during this process are scarce and restricted to the analysis of relatively few transcription factors. Here, we present a description of the expression patterns of Hox genes during the embryonic and larval development of the phoronidPhoronopsis harmeri.Results: We identified sequences of eight Hox genes in the transcriptome ofPh. harmeriand determined their expression pattern during embryonic and larval development using whole mount in situ hybridization. We found that none of the Hox genes is expressed during embryonic development. Instead their expression is initiated in the later developmental stages, when the larval body is already formed. In the investigated initial larval stages the Hox genes are expressed in the non-collinear manner in the posterior body of the larvae: in the telotroch and the structures that represent rudiments of the adult worm. Additionally, we found that certain head-specific transcription factors are expressed in the oral hood, apical organ, preoral coelom, digestive system and developing larval tentacles, anterior to the Hox-expressing territories.Conclusions: The lack of Hox gene expression during early development ofPh. harmeriindicates that the larval body develops without positional information from the Hox patterning system. Such phenomenon might be a consequence of the evolutionary intercalation of the larval form into an ancestral life cycle of phoronids. The observed Hox gene expression can also be a consequence of the actinotrocha representing a “head larva”, which is composed of the most anterior body region that is devoid of Hox gene expression. Such interpretation is further supported by the expression of head-specific transcription factors. This implies that the Hox patterning system is used for the positional information of the trunk rudiments and is, therefore, delayed to the later larval stages. We propose that a new body form was intercalated to the phoronid life cycle by precocious development of the anterior structures or by delayed development of the trunk rudiment in the ancestral phoronid larva.

Background: Brachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopodT. transversa.Results: Transcriptome and genome searches for the 10 target genes in the brachiopodsTerebratalia transversa,Lingula anatina,Novocrania anomala, the bryozoansBugula neritinaandMembranipora membranacea, and the phoronidsPhoronis australisandPhoronopsis harmeriresulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception inL. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genesengrailed,distal-less,ferritin,perlucin,sp1andsp2were shown to be expressed in the biomineralising mantle margin ofT. transversajuveniles.Conclusions: The gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid–bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.

The Cambrian fossil Amiskwia sagittiformis has puzzled palaeontologists for more than a century, but recent re-investigation of its morphology suggested a close relationship with the bilaterian clade Gnathifera, comprising Rotifera, Gnathostomulida and Micrognathozoa. Since Amiskwia has already been considered closely related to Chaetognatha, this new interpretation of its morphology supports recent molecular and developmental studies finding a close phylogenetic relationship between Chaetognatha and Gnathifera. The recent re-description of the jaw apparatus of Amiskwia with the first phylogenetic analysis by Vinther & Parry ( 2019 Vinther, J. & Parry, L. A. 2019. Bilateral jaw elements in Amiskwia sagittiformis bridge the morphological gap between gnathiferans and chaetognaths. Current Biology, 29(5), 881–888. [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] ) found a rather surprising topology with Amiskwia and Chaetognatha being sister groups and nested inside Gnathifera. Furthermore, a subsequent paper from Caron & Cheung ( 2019 Caron, J.-B. & Cheung, B. 2019. Amiskwia is a large Cambrian gnathiferan with complex gnathostomulid-like jaws. Communications Biology, 2, 164. doi:10.1038/s42003-019-0388-4 [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] ) re-described the jaws of Amiskwia as very similar to the configuration found in Gnathostomulida, but did not include any phylogenetic analysis. Here we test the topology of Vinther & Parry with various parsimony and Bayesian analyses, taking into account the new description of Caron & Cheung with careful re-amendment of the matrix of Vinther & Parry. According to our results and the recent findings on the molecular phylogeny of their extant members, we suggest a new systematization of these taxa. We recovered Amiskwia as a stem-group chaetognath within a clade Cucullophora nov., rejecting the Caron & Cheung hypothesis of its close affinity to Gnathostomulida, and found a more consensual topology with monophyletic Gnathifera sister group to Cucullophora, all together forming the clade Chaetognathifera. Furthermore, Rotifera + Micrognathozoa form a clade named Gynognathifera nov. We discuss the characters supporting each clade and the reasons that account for the topology found by Vinther & Parry. Finally, we hope that this carefully amended matrix focused on Gnathifera, Amiskwia and Chaetognatha, together with a formal classification and robust phylogeny, will be of use for future studies on the palaeontology and morphology of these clades.

The remarkable regenerative abilities of flatworms are closely linked to neoblasts – adult pluripotent stem cells that are the only division-competent cell type outside of the reproductive system. Although the presence of neoblast-like cells and whole-body regeneration in other animals has led to the idea that these features may represent the ancestral metazoan state, the evolutionary origin of both remains unclear. Here we show that the catenulid Stenostomum brevipharyngium, a member of the earliest-branching flatworm lineage, lacks conventional neoblasts despite being capable of whole-body regeneration and asexual reproduction. Using a combination of single-nuclei transcriptomics, in situ gene expression analysis, and functional experiments, we find that cell divisions are not restricted to a single cell type and are associated with multiple fully differentiated somatic tissues. Furthermore, the cohort of germline multipotency genes, which are considered canonical neoblast markers, are not expressed in dividing cells, but in the germline instead, and we experimentally show that they are neither necessary for proliferation nor regeneration. Overall, our results challenge the notion that canonical neoblasts are necessary for flatworm regeneration and open up the possibility that neoblast-like cells may have evolved convergently in different animals, independent of their regenerative capacity.