<p>The phylum Priapulida is a small group of marine worms that is allied with the nematodes, kinorhynchs, loriciferans and nematomorphs in a clade called the Cycloneuralia or Introverta. Together with the arthropods they are generally considered to comprise the Ecdysozoa, a clade of moulting animals. A number of recent priapulid species possess features that resemble the predicted Ecdysozoan ancestor. In addition, recent molecular studies have also shown that they are basal within the Ecdysozoa/Cycloneuralia (Garey 2001, Webster et al. 2006). Their putative basal position thus makes priapulids highly interesting research objects for understanding the evolution of Ecdysozoa. </p><p>Earlier investigations of the early embryology of the priapulid <i>Priapulus caudatus</i> are critically revised with the aid of modern techniques and equipment, confirming earlier studies that the early cleavages are highly symmetrical, total, subequal, radial and stereotypical. New results show that up to the sixth cleavage, the spindles are oriented along the animal/vegetal axis at both poles. This unique cleavage pattern has only limited similarities to other animals. During the sixth cleavage two cells move inwards and gastrulation commences. If the mesoderm is derived from both cells, its origin differs from that of many other protostomes.</p><p>Two previously undescribed larval stages of <i>P. caudatus</i>; the light bulb shaped hatchling and the first lorica larva are described. The second lorica larva superficially resembles the previously described type 2 lorica larva (Higgins et al 1993). Differences between the second lorica larva and the type 2 lorica larva, with respect to possible ecophenotypical variation and sub-specialization, are described. </p><p>Preliminary data are presented on musculature development of <i>P. caudatus</i>. Preliminary data have also been obtained on the early development of a second priapulid, <i>Halicryptus spinulosus</i>. Comparison of <i>Halicryptus</i> and <i>Priapulus</i> may help to resolve developmental ground pattern of the priapulids.</p>

A character data set suitable for cladistic analysis of tardigrades at the family level was developed. The data matrix consisted of 50 morphological characters from 15 families of tardigrades and was analyzed by maximum parsimony. Kinorhynchs, loriciferans and gastrotrichs were used as outgroups. The results agree with the currently accepted hypothesis that Eutardigrada and Heterotardigrada are distinct monophyletic groups. Among the eutardigrades, Eoyhypsibiidae was found to be a sister group to Macrobiotidae + Hypsibiidae, while Milnesiidae was the basal eutardigrade family. The basal heterotardigrade family was found to be Oreellidae. Echiniscoideans grouped with some traditional Arthrotardigrada (Renaudarctidae, Coronarctidae + Batillipedidae) suggesting that the arthrotardigrades are not monophyletic. An 18S rRNA phylogenetic hypothesis was developed and supports the monophyly of Heterotardigrada and of Parachela versus Apochela within the Eutardigrada. Mapping of habitat preference suggest that terrestrial tardigrades are the ancestral state. Molecular analysis of a sediment sample with an unusually large population of tardigrades had a higher diversity when compared to manual sorting and counting.

The phylum Priapulida is a small group of marine worms that is allied with the nematodes, kinorhynchs, loriciferans and nematomorphs in a clade called the Cycloneuralia or Introverta. Together with the arthropods they are generally considered to comprise the Ecdysozoa, a clade of moulting animals. A number of recent priapulid species possess features that resemble the predicted Ecdysozoan ancestor. In addition, recent molecular studies have also shown that they are basal within the Ecdysozoa/Cycloneuralia (Garey 2001, Webster et al. 2006). Their putative basal position thus makes priapulids highly interesting research objects for understanding the evolution of Ecdysozoa. Earlier investigations of the early embryology of the priapulid Priapulus caudatus are critically revised with the aid of modern techniques and equipment, confirming earlier studies that the early cleavages are highly symmetrical, total, subequal, radial and stereotypical. New results show that up to the sixth cleavage, the spindles are oriented along the animal/vegetal axis at both poles. This unique cleavage pattern has only limited similarities to other animals. During the sixth cleavage two cells move inwards and gastrulation commences. If the mesoderm is derived from both cells, its origin differs from that of many other protostomes. Two previously undescribed larval stages of P. caudatus; the light bulb shaped hatchling and the first lorica larva are described. The second lorica larva superficially resembles the previously described type 2 lorica larva (Higgins et al 1993). Differences between the second lorica larva and the type 2 lorica larva, with respect to possible ecophenotypical variation and sub-specialization, are described. Preliminary data are presented on musculature development of P. caudatus. Preliminary data have also been obtained on the early development of a second priapulid, Halicryptus spinulosus. Comparison of Halicryptus and Priapulus may help to resolve developmental ground pattern of the priapulids.

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. In this thesis we report on a comprehensive study of the pres- ence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. We observe that loss of individual DNMTs independently occured multiple times across ecdysozoan phyla. In several cases, this resulted in a loss of DNA methylation. In vertebrates, however, there is no single species known which lost DNA methylation. Actually, DNA methylation was greatly expanded after the 1R/2R whole genome duplication (WGD) and became a genome-wide phe- nomena. In our study of vertebrates we are not looking for losses of DNA methyltransferases and DNA methylation but are rather interested in the gain of additional DNA methyltransferase genes. In vertebrates there were a number of WGD. Most vertebrates only underwent two WGD but in the teleost lineage a third round of WGD occured and in some groups, e.g. Salmoniformes and some Cypriniformes even a forth WGD occured. The Carp-specific WGD (4R) is one of the most recent vertebrate WGD and is estimated to have occured 12.4 mya. We performed the most comprehen- sive analysis of the evolution of DNA methyltransferases after vertebrate whole-genome duplications (WGD) so far. We were able to show that the conservation of duplicated DNMT3 genes in Salmoniformes is more diverse than previously believed. We were also able to identify DNA methyltrans- ferases in Cypriniformes which have, due to their recent WGD, quite com- plex genomes. Our results show that the patterns of retained and lost DNA methyltransferases after a forth round of WGD differ between Cypriniformes and Salmoniformes. We also proposed a new nomenclature for teleost DNMT genes which correctly represents the orthology of DNMT genes for all teleost species. Next to these purely computational projects we collaborated with the Aluru lab to investigate the effects of different disturbances on zebrafish DNA methylation. One disturbance is the inactivation of DNMT3aa and DNMT3ab as single knockouts as well as a double knockout. This was the first double knockout of DNMT genes in zebrafish which was ever generated. It allows us to study the subfunctionalization of the two DNMT3a genes their effect on genome-wide DNA methylation. Given our results we hypothesize that DNMT3aa and DNMT3ab can compensate for each other to a high de- gree. DNMT3a genes have likely been subfuntionalized but their loss can be compensated by DNMT3b genes. This compensation by DNMT3b genes works well enough that no notable phenotype can be observed in double knockout zebrafish but a difference is notable on the epigenome level. The second disturbance we studied is the exposure of zebrafish to the toxic chemi- cal PCB126. We detected a moderate level of DNA methylation changes and a much larger effect on gene expression. Similar to previous reports we find little correlation between DNA methylation and gene expression changes. Therefore, while PCB126 exposure has a negative effect on DNA methyla- tion it is likely that other gene regulatory mechanisms play a role as well, possibly even a greater one. How do genes evolve and how are genes regulated are two of the main questions of modern molecular biology. In this thesis we have tried to shed more light on both questions. we have broadly expanded the phylogenetic range of species with a manually curated set of DNA methyltransferases. We have done this for ecdysozoan species which have lost all DNA methylating enzymes as well as for teleost fish which acquired more than ten copies of the, originally, two genes. We were also able to generate new insight into the subfunctionalization of the DNA methylation machinery in zebrafish and how it reacts to environmental effects.:1 Introduction 1.1 Biological introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2 Detecting DNA methylation . . . . . . . . . . . . . . . . . . . . . . . . 7 2 Evolution of DNA methylation across Ecdysozoa 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3 Evolution of DNA methyltransferases after vertebrate whole genome duplications 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4 The effect of DNMT3aa and DNMT3ab knockout on DNA methyla- tion in zebrafish 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 5 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish exposed to Pentachlorobiphenyl 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 5.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 6 Conclusions 6.1 Evolution of DNA methylation across Ecdysozoa . . . . . . . . . . . . . 95 6.2 Evolution of DNA methyltransferases after vertebrate whole genome duplications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 6.3 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish (Danio rerio) exposed to Pentachlorobiphenyl (PCB 126). . . 107 6.4 Knockout of DNMT3aa and DNMT3ab in zebrafish (Danio rerio) . . . . . . 108 Bibliography 119

The Tardigrada are hydrophilous, segmented, molting micrometazoans that occupy a diversity of niches in freshwater, marine, and terrestrial habitats. A sister group of the arthropods, this phylum of bilaterally symmetrical lobopods, most less than 1 mm in length, have a hemocoel, a complete digestive tract, a dorsal gonad with one or two gonoducts, and a dorsal lobed brain with a ventral nerve cord and five ganglia. About 1000 species have been described based on the morphology of sclerified structures, especially the claws and buccal-pharyngeal apparatus. Reproduction occurs through fertilized or unfertilized eggs, with individuals being either gonochoric, unisexual, or hermaphroditic, and eggs are deposited either freely or within the shed exuvium. Parthenogenesis, very frequent in limnic and terrestrial tardigrades, allows them to colonize new territories by passive dispersal of a single individual. Quiescence (cryptobiosis: anhydrobiosis, anoxybiosis, cryobiosis, and osmobiosis) and diapause (encystment and resting eggs) occur during the tardigrade life history. Ecological parameters and global distribution patterns are poorly known or understood. Methods for collection, microscopy, and culturing have been developed.

A sister group of the Arthropoda, the Tardigrada are micrometazoans that occupy a diversity of niches in freshwater, marine, and terrestrial habitats. Commonly called water bears because of their slow, lumbering gait, these molting lobopods have four pairs of legs, usually terminating in claws. Most are less than 1 mm in length, with a complete digestive tract, a dorsal gonad with one or two gonoducts, and a dorsal lobed brain with a ventral nerve cord and four bilobed ganglia, one per leg-bearing metamere. The body cavity (hemocoel) functions in respiration and circulation. Over 1200 species have been described based primarily on the morphology of the claws and buccal-pharyngeal apparatus. Individuals may be either gonochoric, unisexual, or hermaphroditic, with fertilized or unfertilized eggs deposited either freely or within the shed exuvium. Parthenogenesis occurs frequently in limnic and terrestrial tardigrades, allowing them to colonize new territories by passive dispersal of a single individual. Cryptobiosis (anhydrobiosis, anoxybiosis, cryobiosis, and osmobiosis) and diapause (encystment and resting eggs) occur during the life history. Active adults (surrounded by water) and cryptobiotic adults and eggs are primarily dispersed passively, but some active dispersal can also occur. Due to the characteristic patchy distributions of tardigrade populations, little is known about their population dynamics and trophic relationships. Improved methods for collection, microscopy, culturing, and molecular analyses have been have contributed much to our knowledge of tardigrades.