A genomic perspective on variations in the molecular toolkit for development and on the evolution of parthenogenesis in Nematoda

The phylum Nematoda is characterised by a huge diversity of species that exploit almost all habitats on earth. Despite their prevalence in a wide range of different ecosystems, nematodes adhere to a strikingly strict Bauplan with only minor variations, even between two large groups that split more than 400 million years ago. The conservation of the final adult body form is quite special and not common in other animal taxa; this exceptional conservatism in the Bauplan, and the very similar patterns of early development observed in the model organisms C. elegans, P. pacificus and Ascaris together, have led scientist to suggest that these mechanisms of early development are archetypical for the phylum. However, analysis pioneered in the Schierenberg laboratory throughout the last 25 years challenged this view by describing considerable variations of early development in several species from different branches of the phylum. These observations together with data from divergent species in Panarthropoda gave rise to the question whether the molecular toolkit for nematode development could be subject to change as well. In the thesis presented here, this question is addressed from a genomic perspective, assembling and analysing large-scale data from species on different taxonomical levels. Based on these data comparisons have been made ranging from species at phylogenetically antipodal positions in the phylum separated by hundreds of millions of years of evolution to genera in one specific clade of the nema- tode tree, and finally the comparison of two closely related genera. In all these taxa Gene Regulatory Networks (GRNs) of early development are analysed and set into perspective with the common model of the nematode developmental toolkit drawn from C. elegans. I used these assays to test whether recently widely discussed theories on the role of GRNs for development deliver valid predictions for the evolution of early development in Nematoda. In fact, I find that the emerging picture supports such hypotheses of GRN evolution: in many pathways intermediate genetic switches appear to be exchanged by processes collectively called “Developmental System Drift (DSD), while upstream and downstream acting genes are more likely to be conserved. Despite this disparity across Nematoda, an analysis of genes retained across all Bilateria shows that this hugely diverse taxon, comprising Nematoda, could be characterized by aprocess of minimal divergence namely the phase in development when the adult body form is constructed. In Nematoda, parthenogenesis evolved in several genera, with a hotspot in clade IV of the phylum. The data sampled to assess the evolution of development in this thesis are used to elucidate the origin and molecular mechanisms underlying parthenogenesis in the genus Panagrolaimus. While the establishment of a re-shuffling mechanisms of GRNs through DSD does not yet allow us to unravel the distinct molecular mechanisms underpinning the establishment and maintenance of parthenogenesis, we have good evidence that parthenogenetic species in the genus Panagrolaimus are polyploid hybrids. This finding supports the hypothesis that hybridisation is a common route to parthenogenesis in Nematoda, as found in many other taxa as well. Parthenogenesis has also been linked to survival in novel and extreme environments, this would be facilitated in the Panagrolaimus species as they are capable of undergoing cryptobiosis (complete desiccation) in contrat to C.elegans and most other nematodes tested. Exploring the trait from a genomic perspective, we found genes known to be acting in this process in Panagrolaimus, but more importantly an intriguing link to Horizontal Gene Transfer (HGT) was found. Genes acquired through HGT appear to lend Panagrolaimus an adaptive advantage in extreme environments by acting in DNA repair mechanisms, which are important during rehydration. This illustrates the previously underestimated importance of HGT in Metazoa. The genomic and transcriptomic data sampled and assembled for this thesis can serve as a basis for future projects analysing the evolution of developmental systems with regards to GRNs and DSD, as well as detailed analyses of anhydrobiosis and the molecular background of parthenogenesis

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects

Genome sequencing has been democratized by second-generation technologies, and even small labs can sequence metazoan genomes now. In this article, we describe ‘959 Nematode Genomes’—a community-curated semantic wiki to coordinate the sequencing efforts of individual labs to collectively sequence 959 genomes spanning the phylum Nematoda. The main goal of the wiki is to track sequencing projects that have been proposed, are in progress, or have been completed. Wiki pages for species and strains are linked to pages for people and organizations, using machine- and human-readable metadata that users can query to see the status of their favourite worm. The site is based on the same platform that runs Wikipedia, with semantic extensions that allow the underlying taxonomy and data storage models to be maintained and updated with ease compared with a conventional database-driven web site. The wiki also provides a way to track and share preliminary data if those data are not polished enough to be submitted to the official sequence repositories. In just over a year, this wiki has already fostered new international collaborations and attracted newcomers to the enthusiastic community of nematode genomicists. www.nematodegenomes.org

The genome of Romanomermis culicivorax:revealing fundamental changes in the core developmental genetic toolkit in Nematoda

Background: The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. Results: We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. Conclusions: Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model

Fitness Landscape of the Fission Yeast Genome.

The relationship between DNA sequence, biochemical function, and molecular evolution is relatively well-described for protein-coding regions of genomes, but far less clear in noncoding regions, particularly, in eukaryote genomes. In part, this is because we lack a complete description of the essential noncoding elements in a eukaryote genome. To contribute to this challenge, we used saturating transposon mutagenesis to interrogate the Schizosaccharomyces pombe genome. We generated 31 million transposon insertions, a theoretical coverage of 2.4 insertions per genomic site. We applied a five-state hidden Markov model (HMM) to distinguish insertion-depleted regions from insertion biases. Both raw insertion-density and HMM-defined fitness estimates showed significant quantitative relationships to gene knockout fitness, genetic diversity, divergence, and expected functional regions based on transcription and gene annotations. Through several analyses, we conclude that transposon insertions produced fitness effects in 66-90% of the genome, including substantial portions of the noncoding regions. Based on the HMM, we estimate that 10% of the insertion depleted sites in the genome showed no signal of conservation between species and were weakly transcribed, demonstrating limitations of comparative genomics and transcriptomics to detect functional units. In this species, 3'- and 5'-untranslated regions were the most prominent insertion-depleted regions that were not represented in measures of constraint from comparative genomics. We conclude that the combination of transposon mutagenesis, evolutionary, and biochemical data can provide new insights into the relationship between genome function and molecular evolution

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

Endorsing Darwin: global biogeography of the epipelagic goose barnacles Lepasspp. (Cirripedia, Lepadomorpha) proves cryptic speciation

It was Darwin that noted the large intraspecific diversity of the goose barnacle Lepas Linnaeus, 1758 and thought about distinct regional varieties. Today, biogeographic compartmentation is known from marine species, but data from globally occurring species remain scarce. We analysed inter- and intraspecific divergence within the epipelagic rafter Lepas from tropical and temperate oceans by means of two mitochondrial and one nuclear DNA marker. Besides phylogenetic relations, we resolved biogeography and controlling factors. Inhabiting the Southern Hemisphere, Lepas australis Darwin, 1851 shows separate populations from coastal Chile and from circum-Antarctic waters, most probably related to temperature differences in the current systems. The cosmopolitan Lepas anatifera Linnaeus, 1758 displays four regional subgroups (coastal Chile, Northeast Pacific/Oregon, the Southern Hemisphere Indopacific, and the Atlantic), and a global group, which might be an ancestral stem group. The differentiation reflects vicariance effects rooted in geological history: the closure of the Neogene Tethys in the Middle East and at the Panama Isthmus, the installation of the cool Benguela Current, differing Pleistocene currents and temperatures, and modern current systems. The extreme ecological generalists Lepas anserifera Linnaeus, 1767 and Lepas pectinata Spengler, 1793 are not differentiated, and might represent true global species. In conclusion, compartmentation of the oceans acts at the species level according to ecospace limits. For Lepas, the multitude of barriers favours allopatric speciation

Conserved Patterns in Developmental Processes and Phases, Rather than Genes, Unite the Highly Divergent Bilateria

Bilateria are the predominant clade of animals on Earth. Despite having evolved a wide variety of body plans and developmental modes, they are characterized by common morphological traits. By default, researchers have tried to link clade-specific genes to these traits, thus distinguishing bilaterians from non-bilaterians, by their gene content. Here we argue that it is rather biological processes that unite Bilateria and set them apart from their non-bilaterian sisters, with a less complex body morphology. To test this hypothesis, we compared proteomes of bilaterian and non-bilaterian species in an elaborate computational pipeline, aiming to search for a set of bilaterian-specific genes. Despite the limited confidence in their bilaterian specificity, we nevertheless detected Bilateria-specific functional and developmental patterns in the sub-set of genes conserved in distantly related Bilateria. Using a novel multi-species GO-enrichment method, we determined the functional repertoire of genes that are widely conserved among Bilateria. Analyzing expression profiles in three very distantly related model species-D. melanogaster,D. rerioandC. elegans-we find characteristic peaks at comparable stages of development and a delayed onset of expression in embryos. In particular, the expression of the conserved genes appears to peak at the phylotypic stage of different bilaterian phyla. In summary, our study illustrate how development connects distantly related Bilateria after millions of years of divergence, pointing to processes potentially separating them from non-bilaterians. We argue that evolutionary biologists should return from a purely gene-centric view of evolution and place more focus on analyzing and defining conserved developmental processes and periods