Deciphering the rapid emergence of bilaterian animals around the time of the Cambrian Explosion and reconstructing the interrelationships of animal groups have long been two of the most elusive problems in Zoology. This thesis concerns the phylogenetic interrelationships within and among Acoela and Nemertodermatida, two groups of small worms that are believed to be basal bilaterians and which may provide important clues for understanding the early evolution of animals. In addition to trying to resolve the phylogenetic positions of these groups, major focus is put on inferring how ancestral animals might have looked, given the phylogenetic hypotheses put forward. The data used to infer phylogenies include nuclear ribosomal DNA, the mitochondrial COI gene and microRNAs. Based on phylogenetic analyses of a large number of 18S SSU ribosomal DNA sequences, it is proposed that Cnidaria is the sister taxon to Bilateria. Poor taxon sampling is suggested to be one of the reasons for why earlier assessments of the interrelationships among the most basal animal groups have yielded many conflicting results using the same gene. Analyses of new 18S SSU rDNA and 28S LSU rDNA sequences from six of the nine known species of nemertodermatids corroborate earlier indications that Acoela and Nemertodermatida are not sister taxa, as once thought. Being separate basal bilaterian animal groups, it is suggested that the last common ancestor of all bilaterians shared much of their comparatively simple morphology. Many methods are deployed to assess whether the phylogenetic results are mainly due to long-branch attraction, but no indication of this artifact is detected. The first comprehensive phylogenetic framework of Acoela is reconstructed from the 18S SSU, 28S LSU and COI genes, in combination with morphological data. The ancestral acoel worm is reconstructed using Bayesian methods and morphological observations in extant species. Two indeces, posterior similarity and reconstruction signal, are implemented to assess how similar different species are to the last common ancestor of all acoels and illustrate how clearly different characters or nodes are reconstructed. It is suggested that the ancestral acoel looked much like extant species of Diopisthoporus. The phylogenetic positions of Acoela and Nemertodermatida are assessed using new data on microRNAs in the acoel Hofstenia miamia and the nemertodermatid Meara stichopi. Acoela and Nemertodermatida are again found to be basal bilaterians, in congruence with earlier results. Using the work-flow and indeces developed earlier, it is concluded that the bilaterian ancestral microRNA repertoire can not yet be reconstructed with high confidence. All papers stress the importance of inclusive taxon sampling for making generalized inferences about ancestral features in animals.

Nemertodermatida is a group of microscopic marine worm-like animals that live as part of the marine meiofauna in sandy or muddy sediments; one species lives commensally in a holothurian. These benthic worms were thought to disperse passively with ocean currents, resulting in little speciation and thus wide or even cosmopolitan distributions. Individuals occur in low abundance and have few light microscopically available characters, which altogether may explain why only eight species had been described between the discovery of the taxon in 1930 and this thesis. We used molecular methods to address the diversity and phylogeny of this group for the first time. In a study of two nominal species with samples from all around the world, a high degree of cryptic speciation was discovered and several new species described. Diagnoses were based on molecular data complemented by morphological characters, where available. Given the patchy geographical record it can be assumed that the majority of the biodiversity of Nemertodermatida is yet to be described. A phylogenetic study including all but three known species revealed a deep divergence between the two families of Nemertodermatida but non-monophyly of the taxon was rejected by an Approximately Unbiased test. Confocal laser scanning microscopic studies of several species show that the pattern of the body-wall musculature and the nervous system are specific for different genera. The muscular system of all species consists of a basic orthogonal grid with specific diagonal musculature and specialized muscles associated with body openings. The mouth appears to be transient feature in Nemertodermatida, developing only after hatching and being reduced again in mature worms. The nervous system is highly variable with very different ground patterns between the genera, such as an epidermal net, a centralized neuropile or a commissural brain. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4. Manuscript.</p>