Sommer, Ralf J. (2011) International Worm Meeting "Molecular phylogeny and divergence time estimates for beetle-associated Pristionchus nematodes."

Sommer, Ralf J.

[International Worm Meeting, 2011]

Pristionchus pacificus has been established as a model system in evolutionary developmental biology (evo-devo) and for comparison to C. elegans. Recent studies expanded the evo-devo work to ecology and population genetics. P. pacificus and related species have a well-defined association with scarab beetles: Sampling of more than 20,000 scarab beetles from around the world resulted in the isolation of more than 8,000 Pristionchus isogenic female lines. Mating experiments and molecular sequence analysis identified 26 species to date. We provide a molecular phylogenetic framework based on nearly 11,000 characters. Studies on La Reunion, an Island with a unique P. pacificus biodiversity hotspot, provide a case study to link population genetics with ecology and evo-devo. We obtained more than 400 wild isolates of P. pacificus and carried out microsatellite analysis of 21 markers. These studies indicate four major biogeographic clades of P. pacificus. La Reunion represents the only geographic area with P. pacificus strains being present in all four clades. This finding is best explained by P. pacificus invading the island independently with different beetle vectors, such as Oryctes, Amneidus and Maladera (Herrmann et al., 2010). We assessed the molecular phylogeny of P. pacificus and used mutation accumulation line approaches to provide divergence time estimates. Mutation rates were assessed first, by mitochondrial DNA analysis and second, from representative microsatellite markers. Mitochondrial DNA analysis suggests a minimal divergence time for P. pacificus of 105 to 106 generations (Molnar et al., 2011). Similarly, microsatellite markers are used to robustly provide minimal divergence time estimates for closely related strains from La Reunion. This includes a first attempt for a serious analysis of the population size of P. pacificus.

Ralf J. Sommer (2006) WormBook "Pristionchus pacificus."

Ralf J. Sommer

[WormBook, 2006]

In the last decade, nematodes other than C. elegans have been studied intensively in evolutionary developmental biology. A few species have been developed as satellite systems for more detailed genetic and molecular studies. One such satellite species is the diplogastrid nematode Pristionchus pacificus. Here, I provide an overview about the biology, phylogeny, ecology, genetics and genomics of P. pacificus.

Ralf Sommer (2006) Development & Evolution Meeting "Evolutionary Developmental Biology In Nematodes: Comparing Pristionchus pacificus To C. elegans"

Ralf Sommer

[Development & Evolution Meeting, 2006]

Cell fate specification and cell-cell signaling have been well studied during the development of C. elegans and provide a paradigm in evolutionary developmental biology. We have developed Pristionchus pacificus as a satellite organism in evolutionary developmental biology, in which forward and reverse genetic studies can be performed. Additionally, a genomic platform with an integrated physical and genetic map and an 8 X coverage of the P. pacificus genome sequence is available that allows detailed comparisons to C. elegans. The comparison between P. pacificus and C. elegans, two nematodes that shared a last common ancestor 200-300 million years ago, indicates major differences in the patterning mechanisms underlying developmental processes, i.e. vulva formation, gonad development and the regulation of dauer formation. Our analysis of vulva development indicates three major sets of differences. First, the two nematodes contain different molecular modules. For example, P. pacificus contains an ancestral HAIRY/GROUCHO module that is important in the regulation of vulva patterning and that no longer exists in C. elegans. Second, orthologous developmental control genes and signaling pathways have different functions. In C. elegans, EGF/RAS and Wnt signaling are crucial for vulva induction. In contrast in P. pacificus, mutations in Ppa-lin-17/Frizzled and Ppa-groucho/unc-37 result in a multivulva phenotype indicating a role in a negative signaling process. Third, at the cellular level, homologous cells perform species-specific cell-cell interactions reflecting the molecular differences in signaling activity. To complement our macro-evolutionary comparison, we initiated ecological studies. In contrast to C. elegans that lives as a soil-dwelling species, Pristionchus nematodes occur in strong association with beetles, in particular cockchafers, dung beetles and Colorado potato beetles. In this ecological context, we study the genetic control of dauer formation and olfaction to learn how during the evolution of this novel ecological association patterning mechanisms have changed. Interestingly, Pristionchus species but not C. elegans is attracted by various insect sex pheromones. Currently, we are using a genetic approach to determine the molecular mechanism of the nematode - insect interaction.

Ralf J. Sommer (2005) WormBook "Evolution of development in nematodes related to C. elegans."

Ralf J. Sommer

[WormBook, 2005]

The knowledge about C. elegans provides a paradigm for comparative studies. Nematodes are very attractive in evolutionary developmental biology given the species richness of the phylum and the easiness with which several of these species can be cultured under laboratory conditions. Embryonic, gonad, vulva and male tail development were studied and compared in nematodes of five different families, providing a detailed picture of evolutionary changes in development. In particular, vulva development has been studied in great detail and substantial differences in the cellular, genetic and molecular mechanisms have been observed between C. elegans and other nematodes. For example, vulva induction relies on the single anchor cell in C. elegans, whereas a variety of different cellular mechanisms are used in related species. In recent years, a few species have been developed as satellite systems for detailed genetic and molecular studies, such as Oscheius tipulae and Pristionchus pacificus.

Sommer RJ et al. (1994) Worm Breeder's Gazette "Evolution of Vulva-Formation: Part II: Species With a Central Vulva"

Sommer RJ, Sternberg PW

[Worm Breeder's Gazette, 1994]

Evolution of vulva-formation: Part II: Species with a central vulva Ralf J. Sommer & Paul W. Sternberg, California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125

Ralf J Sommer et al. (2002) Worm Breeder's Gazette "Towards a Pristionchus genome map- I - P. pacificus BAC Library construction and end sequencing of BAC clones"

Christa Lanz, Taco Jesse, Stephan C Schuster, Heike Keller, Gunther Raddatz, Ralf J Sommer

[Worm Breeder's Gazette, 2002]

In order to facilitate the easier cloning of genes in the satellite model system Pristionchus pacificus , we have initiated a genomic approach by constructing genetic and physical maps of Pristionchus pacificus . An essential prerequisite for a good genomics approach is the availability of a good genomic library with large insert sizes. We constructed a BAC library of Pristionchus pacificus . The library contained 13, 440 clones in total and was a result of 4 different ligations. The average insert size of the clones is 128 kb. Insert sizes ranged between 100-180kb. We estimate the genome coverage of the library to be approximately 8 times. End sequencing of the BAC clones was done at the Genome Centre of the MPI Tubingen. Uptil now 6000 BAC clones have been end sequenced. On an average approximately 600 bp were read from each BAC end. The sequence was checked for quality using the PHRED/PHREP protocol. The total length of the BAC ends sequenced was approximately 10 Mb. The GC content of the sequence was 47%. From the 11271 ends sequenced, 8232 BAC ends gave no hits and 1129 gave hits to the non-redundant NCBI database.

Sommer RJ et al. (1994) Worm Breeder's Gazette "Evolution of Vulva Formation: Part IV: Variation in AC Position Can Cause a Shift of Vulva Formation Towards P(4-6).p."

Sternberg PW, Sommer RJ

[Worm Breeder's Gazette, 1994]

Evolution of vulva formation: Part IV: Variation in AC position can cause a shift of vulva formation towards p(4- 6).p Ralf J. Sommer & Paul W. Sternberg, HHMI & California Institute of Technology, Division of Biology 156-29, Pasadena, CA

Susoy, Vladislav et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "EVOLUTIONARY DIVERSIFICATION THROUGH THE GAIN AND LOSS OF DEVELOPMENTAL PLASTICITY"

Sommer, Ralf J., Susoy, Vladislav, Ragsdale, Erik J.

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Developmental plasticity is common among plants and animals, yet its role in mediating evolutionary processes is debated. Several species of Rhabditina, including Pristionchus pacificus, can execute two alternative mouth phenotypes, one of which is associated with predatory feeding. Studies in P. pacificus have revealed that environmental factors act through a conserved genetic pathway that enables a rapid developmental response to the environment (Bento et al., 2010). In addition, a developmental switch that controls the expression of the alternative mouth phenotypes was recently identified (Ragsdale et al., 2013). In contrast, little is known about the macroevolutionary potential of the mouth plasticity. We studied the relationship between plasticity and morphological change by a macroevolutionary analysis of nematode mouthparts when accompanied by a dimorphism. To test whether plasticity facilitates or hinders morphological change, we analyzed variation in form and complexity in 90 nematode species with or without a mouth dimorphism. Our analyses revealed a two-step process of morphological diversification associated with the gain and loss of plasticity. First, acquisition of a dimorphism was accompanied by an increase in complexity, including structural innovations such as moveable teeth. Second, the fixation of a single mouth-phenotype in several nematode lineages was associated with a decrease in mouth complexity but a sharp increase in evolutionary rates when measured as change of shape and size. Thus, plasticity facilitates phenotypic diversification by fostering evolutionary novelties, whereas subsequent loss of the dimorphism enables acceleration of evolution by releasing novel morphologies from developmental constraints. 1. G. Bento, A. Ogawa, R. J. Sommer. Nature 466, 494-497 (2010). 2. E. J. Ragsdale, M. R. Muller, C. Rodelsperger, R. J. Sommer, Cell 155, 922-933 (2013).

Wang, Xiaoyue et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "A complex Network of Wnt Signaling with an unusual Wiring regulates the Induction of Vulva Formation in the Nematode P. pacificus."

Sommer, Ralf, Wang, Xiaoyue

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

In C. elegans , vulva formation has been intensively studied and can serve as a paradigm for evo-devo studies. We have developed Pristionchus pacificus as a model organism in evo-devo . While in C. elegans EGF induces vulva development, forward and reverse genetic experiments revealed that Wnt signaling is crucial for vulva induction in P. pacificus . A Ppa-bar-1/-catenin mutant is completely vulvaless. Multiple Wnt ligands and receptors play a redundant role in vulva induction including Ppa-egl-20 /Wnt. Two striking features of P. pacificus Wnt signaling are a negative role of Ppa-lin-17/Frizzled , mutations in which result in a multivulva phenotype, and that a mutation in Ppa-egl-20 can suppress the Ppa-lin-17 phenotype. Such genetic interactions suggest a role of this Frizzled receptor in ligand sequestration. Interestingly, Ppa-egl-20 is only expressed in the rectal region, similar to C. elegans , representing the first inductive ligand for vulva induction that is expressed outside the gonad. To further elucidate the molecular mechanisms of P. pacificus vulva induction, we combined forward genetics and transformation technology. First, a transgenic approach using heat-shock induced Ppa-egl-20 revealed that this Wnt ligand is sufficient for vulva induction. Second, mutations in additional multivulva genes have been cloned. We will report genetic and biochemical experiments, which indicate that changes in ligand-receptor interactions were crucial for the evolution of Wnt signaling in nematodes. Together, this study shows that Wnt signaling during P. pacificus vulva induction i) represents an unusual complexity, ii) consists of a novel wiring involving ligand sequestration and iii) requires novel protein domains in o therwise conserved genes/proteins of the Wnt signaling pathway.

Ogawa, Akira et al. (2009) International Worm Meeting "Genetic analysis of dauer formation in Pristionchus pacificus reveals conserved and diverse aspects of signaling mechanisms."

Ogawa, Akira, Sommer, Ralf

[International Worm Meeting, 2009]

Despite the wealth of knowledge of C. elegans dauer formation, regulation of dauer formation in other nematode species is relatively poorly understood. To address how environmental regulation of dauer formation evolved, we are studying dauer formation in the satellite model nematode Pristionchus pacificus. P. pacificus shares with C. elegans most of the advantageous features of experimental organisms and has genetic tools such as forward and reverse genetics, a complete genome, and transgenic techniques. In the wild P. pacificus associates with scarab beetles as dauer larvae and occupies a distinct ecological niche from C. elegans. Since dauer formation play critical roles in the adaptive strategy of P. pacificus, one can expect many evolutionary novelties in P. pacificus dauer formation. Also genetic analysis of dauer formation in P. pacificus may lead to identification of conserved genetic components of dauer formation that are missed in C. elegans studies. This is because multiple genes may be involved in the same step of the regulatory cascade (redundancy) or there may be genes that are involved in both dauer formation and earlier development (pleiotropy). Such genes are hard to identify in conventional genetic and RNAi screens and studies in P. pacificus that may have different patterns of redundancy and pleiotropy might help identify such genes. So far we have shown that i) P. pacificus uses a distinct pheromone(s) from C. elegans to sense the population density ii) An endocrine module involving dafachronic acids (DAs) and DAF-12 controls dauer formation in P. pacificus. The latter finding was further extended to infective larva formation of the parasitic nematode Strongyloides papillosus. Exogenous administration of D7-DA completely suppresses the formation of infective larva in S. papillosus suggesting infective and dauer larvae share a common evolutionary origin. To elucidate the genes that control P. pacificus dauer formation we screened daf-c and daf-d mutants, and obtained more than 10 strains of each class. In a small-scale screen for daf-c mutants, we obtained several fully penetrant daf-c strains that are relatively rare in C. elegans, as well as partially penetrant strains. All the daf-c strains tested could be at least partially rescued by exogenous administration of D7-dafachronic acid, suggesting they have a mutation in a gene upstream of DA/DAF-12. Interestingly the fully penetrant daf-c strains we obtained did not respond to up to 250 nM of D4-dafachronic acid. Positional mapping of the gene responsible for one of the daf-c strains is ongoing.