Revisiting metazoan phylogeny with genomic sampling of all phyla

Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.

Detailed reconstruction of the nervous and muscular system of Lobatocerebridae with an evaluation of its annelid affinity

BACKGROUND

The microscopic worm group Lobatocerebridae has been regarded a 'problematicum', with the systematic relationship being highly debated until a recent phylogenomic study placed them within annelids (Curr Biol 25: 2000-2006, 2015). To date, a morphological comparison with other spiralian taxa lacks detailed information on the nervous and muscular system, which is here presented for Lobatocerebrum riegeri n. sp. based on immunohistochemistry and confocal laser scanning microscopy, supported by TEM and live observations.

RESULTS

The musculature is organized as a grid of longitudinal muscles and transverse muscular ring complexes in the trunk. The rostrum is supplied by longitudinal muscles and only a few transverse muscles. The intraepidermal central nervous system consists of a big, multi-lobed brain, nine major nerve bundles extending anteriorly into the rostrum and two lateral and one median cord extending posteriorly to the anus, connected by five commissures. The glandular epidermis has at least three types of mucus secreting glands and one type of adhesive unicellular glands.

CONCLUSIONS

No exclusive "annelid characters" could be found in the neuromuscular system of Lobatocerebridae, except for perhaps the mid-ventral nerve. However, none of the observed structures disputes its position within this group. The neuromuscular and glandular system of L. riegeri n. sp. shows similarities to those of meiofaunal annelids such as Dinophilidae and Protodrilidae, yet likewise to Gnathostomulida and catenulid Platyhelminthes, all living in the restrictive interstitial environment among sand grains. It therefore suggests an extreme evolutionary plasticity of annelid nervous and muscular architecture, previously regarded as highly conservative organ systems throughout metazoan evolution.

New Austrognathiidae (Gnathostomulida: Conophoralia) from Hong Kong and Japan: microscopic anatomy, ultrastructure and evolutionary implications

We describe two new species, Austrognathia glandifera and Austrognatharia orientis using observations on squeezed, live specimens as well as histological sections and transmission electron microscopy. The protonephridia of Austrognatharia orientis are composed of a terminal cell, a canal cell, and a nephroporus cell. The monociliated terminal cell constitutes the so-called filtration area. The canal cell harbors the lacunar system and the protonephridial duct, which is surrounded by six filamentous rods, which originate external to and in between the microvilli of the terminal cell and stretch along the entire length of the canal cell. The female copulatory organs of the investigated species are very different. Austrognathia glandifera has a bursa and a vagina whereas A. orientis only has a weakly defined bursal tissue and no detectable vagina. The bursa is divided into an anterior and a posterior part; at the anterior end a special area is formed by interdigitations of the cells of the bursal wall. The male copulatory organs in the Conophoralia are uniform, composed of an anterior, glandular portion consisting of a proximal part with medium-grained and a distal part with coarse-grained appearance and a penis that is delineated by a basal lamina and has an ejaculatory duct as well as a gonopore. Parenchymal cells are present and serve to embed the bursa and the male copulatory organ dorsolaterally. Our data on the fine structure of various tissues indicate that the Conophoralia are the "less derived" sister taxon of the Scleroperalia.

An anatomical description of a miniaturized acorn worm (hemichordata, enteropneusta) with asexual reproduction by paratomy

The interstitial environment of marine sandy bottoms is a nutrient-rich, sheltered habitat whilst at the same time also often a turbulent, space-limited, and ecologically challenging environment dominated by meiofauna. The interstitial fauna is one of the most diverse on earth and accommodates miniaturized representatives from many macrofaunal groups as well as several exclusively meiofaunal phyla. The colonization process of this environment, with the restrictions imposed by limited space and low Reynolds numbers, has selected for great morphological and behavioral changes as well as new life history strategies.Here we describe a new enteropneust species inhabiting the interstices among sand grains in shallow tropical waters of the West Atlantic. With a maximum body length of 0.6 mm, it is the first microscopic adult enteropneust known, a group otherwise ranging from 2 cm to 250 cm in adult size. Asexual reproduction by paratomy has been observed in this new species, a reproductive mode not previously reported among enteropneusts. Morphologically, Meioglossus psammophilus gen. et sp. nov. shows closest resemblance to an early juvenile stage of the acorn worm family Harrimaniidae, a result congruent with its phylogenetic placement based on molecular data. Its position, clearly nested within the larger macrofaunal hemichordates, suggests that this represents an extreme case of miniaturization. The evolutionary pathway to this simple or juvenile appearance, as chiefly demonstrated by its small size, dense ciliation, and single pair of gill pores, may be explained by progenesis. The finding of M. psammophilus gen. et sp. nov. underscores the notion that meiofauna may constitute a rich source of undiscovered metazoan diversity, possibly disguised as juveniles of other species.

New characters in the Gnathostomulid mouth parts revealed by scanning electron microscopy

An analysis with SEM of the mouth parts of 16 species belonging to 10 genera of Gnathostomulida resulted in the following new characters and conclusions: 1) At least in the genus Haplognathia, jaw teeth that are visible by conventional light microscopy are composed of the same aggregated needle-like denticles that are found, often in large numbers, on the basal plates of many filospermoid species. 2) Other new ultrastructural tooth features include the tricuspid basal plate teeth in Problognathia minima, tripartite teeth in Austrognathia and Austrognatharia, and the clear separation, in the Gnathostomula basal plate, of a mediodorsal set of teeth from a more extensive rostroventral set. 3) Three rows of teeth, as typical for Gnathostomulidae and Austrognathiidae, are also present in the filospermoid Haplognathia filum. 4) The wide range of geographic variation in Haplognathia ruberrima is confirmed by significant differences in jaw teeth between specimens from Belize and Bermuda. 5) A compartmentalized involucrum is present in Labidgonathia longicollis. 6) A pair of lamellae addentales, until now only known from Valvognathia pogonostoma, was found in Tenuignathia rikerae, Problognathia minima, and probably also Labidognathia rikerae. 7) In all gnathostomulids, the lamella symphysis is composed of identical rods that are considered homologous with those in the mouth parts of Rotifera and Micrognathozoa.

On the origin of sex as vaccination

In the theory of the origin of sex as vaccination, I propose that the eukaryote genome accreted from prokaryan symbiont genomes in numerous rounds of lateral gene transfer during which sex diverged from unilateral parasitic infection, as an increasingly ritualized, reciprocal vaccination against superinfection. Sex-as-syngamy (fusion sex) arose when infected proto-eukaryan hosts began swapping nuclearized genomes containing coevolved, vertically transmitted ("attenuated") symbionts that conveyed protection against horizontal superinfection by more virulent symbionts. Sex-as-meiosis (fission sex) evolved as a host strategy to uncouple (and thereby emasculate) the acquired symbiont genomes. The chimeric nature, distribution over discrete chromosomes, and mosaic composition of the eukaryan nuclear genome derive from multiple rounds of acquiring and uncoupling prokaryan genomes. Genome compatibility-based recognition of self and mates came to define sex, mate choice, and the biological species. By generating unique individuality, sex now persists as an elaborate (hence tamper-proof) periodic device for an organism to thwart both endo- and exogenous challengers, and stay ahead of an environment whose capriciousness may largely result from the success of its own forebears.

Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.