Opposing forces of A/T-biased mutations and G/C-biased gene conversions shape the genome of the nematode Pristionchus pacificus.

Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation.

Characterization of genetic diversity in the nematode Pristionchus pacificus from population-scale resequencing data.

The hermaphroditic nematode Pristionchus pacificus is an established model system for comparative studies with Caenorhabditis elegans in developmental biology, ecology, and population genetics. In this study, we present whole-genome sequencing data of 104 P. pacificus strains and the draft assembly of the obligate outcrossing sister species P. exspectatus. We characterize genetic diversity within P. pacificus and investigate the population genetic processes shaping this diversity. P. pacificus is 10 times more diverse than C. elegans and exhibits substantial population structure that allows us to probe its evolution on multiple timescales. Consistent with reduced effective recombination in this self-fertilizing species, we find haplotype blocks that span several megabases. Using the P. exspectatus genome as an outgroup, we polarized variation in P. pacificus and found a site frequency spectrum (SFS) that decays more rapidly than expected in neutral models. The SFS at putatively neutral sites is U shaped, which is a characteristic feature of pervasive linked selection. Based on the additional findings (i) that the majority of nonsynonymous variation is eliminated over timescales on the order of the separation between clades, (ii) that diversity is reduced in gene-rich regions, and (iii) that highly differentiated clades show very similar patterns of diversity, we conclude that purifying selection on many mutations with weak effects is a major force shaping genetic diversity in P. pacificus.

Quantitative assessment of the nematode fauna present on Geotrupes dung beetles reveals species-rich communities with a heterogeneous distribution.

Pristionchus spp. nematodes exhibit several traits that might serve as pre-adaptations to parasitism. Under harsh environmental conditions, these nematodes can arrest development and form dauer larvae. In addition, they have been shown to live in necromenic association with a range of beetles, including dung beetles ( Geotrupes stercorosus ) on which, for example, Pristionchus entomophagus is commonly found. It has been argued that the formation of dauer larvae and the association with invertebrates represent intermediate steps towards parasitism. To better understand necromenic associations, and to gain information on Pristionchus spp. abundance and the general species composition on dung beetles, we extracted all the nematode fauna present on 114 individuals of G. stercorosus. By direct sequencing using the 18S SSU, we provide a barcode for all nematodes isolated from the beetle samples. In total, 5,002 dauer-stage nematodes were sequenced, which included Pristionchus spp., Koerneria spp. (Diplogastridae), Pelodera spp. (Rhabditidae), and Strongyloidea as well as Spirurida. Intensities of infection varied from over 1,000 nematodes isolated from a single G. stercorosus to none, with Pelodera spp. being the most abundant group isolated. This study presents the first quantitative data on the Pristionchus spp. infection of beetles.

Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences.

Nematodes and bacteria are major components of the soil ecosystem. Many nematodes use bacteria for food, whereas others evolved specialized bacterial interactions ranging from mutualism to parasitism. Little is known about the biological mechanisms by which nematode-bacterial interactions are achieved, largely because in the laboratory nematodes are often cultured under artificial conditions. We investigated the bacterial interactions of nematodes from the genus Pristionchus that have a strong association with scarab beetles. Pristionchus has a different feeding strategy than Caenorhabditis and meta-genomic 16S sequence analysis of Pristionchus individuals showed a diversity of living bacteria within the nematode gut and on the nematode cuticle. Twenty-three different bacterial strains were isolated from three Pristionchus-beetle associations and were used to study nematode-bacterial interactions under controlled laboratory conditions. We show a continuum of bacterial interactions from dissemination, to reduction in brood size and nematode mortality caused by bacteria derived from insect hosts. Olfactory discrimination experiments show distinct chemoattraction and fitness profiles of Pristionchus nematodes when exposed to different bacteria. For example, Pristionchus pacificus avoids Serratia marcescens possibly because of pathogenicity. Also, P. pacificus avoids Bacillus thuringiensis and insect pathogenic bacteria but is resistant to the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa, unlike Caenorhabditis elegans. Pristionchus specifically recognize and respond to bacteria that cause ill health. Bringing the nematode-bacterial interaction into the laboratory allows detailed functional studies, including the genetic manipulation of the interaction in both nematodes and bacteria.