Despite rapid advances in the study of metazoan evolutionary history [1], phylogenomic analyses have so far neglected a number of microscopic lineages that possess a unique combination of characters and are thus informative for our understanding of morphological evolution. Chief among these lineages are the recently described animal groups Micrognathozoa and Loricifera, as well as the two interstitial "Problematica" Diurodrilus and Lobatocerebrum [2]. These genera show a certain resemblance to Annelida in their cuticle and gut [3, 4]; however, both lack primary annelid characters such as segmentation and chaetae [5]. Moreover, they show unique features such as an inverted body-wall musculature or a novel pharyngeal organ. This and their ciliated epidermis have led some to propose relationships with other microscopic spiralians, namely Platyhelminthes, Gastrotricha, and in the case of Diurodrilus, with Micrognathozoa [6, 7]-lineages that are grouped by some analyses into "Platyzoa," a clade whose status remains uncertain [1, 8-11]. Here, we assess the interrelationships among the meiofaunal and macrofaunal members of Spiralia using 402 orthologs mined from genome and transcriptome assemblies of 90 taxa. Lobatocerebrum and Diurodrilus are found to be deeply nested members of Annelida, and unequivocal support is found for Micrognathozoa as the sister group of Rotifera. Analyses using site-heterogeneous substitution models further recover a lophophorate clade and position Loricifera + Priapulida as sister group to the remaining Ecdysozoa. Finally, with several meiofaunal lineages branching off early in the diversification of Spiralia, the emerging concept of a microscopic, acoelomate, direct-developing ancestor of Spiralia is reviewed.

The Figure 1 legend of this article contains an erroneous citation to a nonexistent Dryad accession intended to store large files such as the total Orthologous MAtrix (OMA) orthogroups used to derive our supermatrices, the supermatrices themselves, supplementary Newick trees (i.e., those shown in summary form in Figures 1B and 1C), and full output from analyses such as those performed in PartitionFinder and ExaML. Such a supplementary data accession, with metadata notes to guide interested users, is now available through the Harvard Dataverse project at https://doi.org/10.7910/DVN/LW4GS4.

The causes and consequences of genome reduction in animals are unclear because our understanding of this process mostly relies on lineages with often exceptionally high rates of evolution. Here, we decode the compact 73.8-megabase genome of Dimorphilus gyrociliatus, a meiobenthic segmented worm. The D. gyrociliatus genome retains traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit and traces of ancestral bilaterian linkage. Unlike some other animals with small genomes, the analysis of the D. gyrociliatus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene-dense D. gyrociliatus genome presents a divergent Myc pathway, a key physiological regulator of growth, proliferation and genome stability in animals. Altogether, our results uncover a conservative route to genome compaction in annelids, reminiscent of that observed in the vertebrate Takifugu rubripes.

Animal genomes vary in size by orders of magnitude 1 . While genome size expansion relates to transposable element mobilisation 2-5 and polyploidisation 6-9 , the causes and consequences of genome reduction are unclear 1 . This is because our understanding of genome compaction relies on animals with extreme lifestyles, such as parasites 10,11 , and free-living animals with exceptionally high rates of evolution 12-15 . Here, we decode the extremely compact genome of the annelid Dimorphilus gyrociliatus, a morphologically miniature meiobenthic segmented worm 16 . With a ~68 Mb size, Dimorphilus genome is the second smallest ever decoded for a free-living animal. Yet, it retains many traits classically associated with larger and slower-evolving genomes, such as an ordered, intact Hox cluster, a generally conserved developmental toolkit, and traces of ancestral 3 bilaterian linkage. Unlike animals with small genomes, the analysis of Dimorphilus epigenome revealed canonical features of genome regulation, excluding the presence of operons and trans-splicing. Instead, the gene dense Dimorphilus genome presents divergent kynurenine and Myc pathways, key physiological regulators of growth, proliferation and genome stability in animal cells that can cause small body size when impaired 17-21 . Altogether, our results uncover a novel, conservative route to extreme genome compaction, suggesting a mechanistic relationship between genome size reduction and morphological miniaturisation in animals.Animals, and eukaryotes generally, exhibit a striking range of genome sizes across species 1 , seemingly uncorrelated with morphological complexity and gene content, which has been deemed the "C-value enigma" 22 . Animal genomes often increase in size mobilising their transposable element (TE) repertoire (e.g. in rotifers 2 , chordates 3,4 and insects 5 ) and through chromosome rearrangements and polyploidisation (e.g. in vertebrates and teleosts 6-8 , and insects 9 ), which is usually counterbalanced through TE removal 23 , DNA deletions 24,25 and rediploidisation 26 . Although the adaptive impact of these changes is complex and probably often influenced by neutral nonadaptive population dynamics 27 , genome expansions might also increase the evolvability of a lineage by providing new genetic material that can stimulate species radiation 6 and the evolution of new genome regulatory contexts 28 and gene architectures 29 . By contrast, the adaptive value of genome compaction is more debated and hypotheses are often based on correlative associations 1 , e.g. with changes in metabolic 30 and developmental rates 31 , cell sizes 1,32 , and the evolution of radically new lifestyles (e.g. powered flight in birds and bats 25,33 , and parasitism in nematodes 11 and orthonectids 10 ).Besides, extreme genomic compaction leading to minimal genome sizes, as in some freeliving species of nematodes 34 , tardigrades 35 and appendicularians 4,36 , co-occurs with 4 prominent changes in gene repertoire 37,38 , genome architecture (e.g. loss of macrosynt...

BackgroundThe 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.ResultsThe 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.ConclusionsNo 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0531-x) contains supplementary material, which is available to authorized users.