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opencc-zeroDec 2013View details →

Data from: Reproductive assurance drives transitions to self-fertilization in experimental Caenorhabditis elegans

Background: Evolutionary transitions from outcrossing between individuals to selfing are partly responsible for the great diversity of animal and plant reproduction systems. The hypothesis of 'reproductive assurance' suggests that transitions to selfing occur because selfers that are able to reproduce on their own ensure the persistence of populations in environments where mates or pollination agents are unavailable. Here we test this hypothesis by performing experimental evolution in Caenorhabditis elegans. Results: We show that self-compatible hermaphrodites provide reproductive assurance to a male-female population facing a novel environment where outcrossing is limiting. Invasions of hermaphrodites in male-female populations, and subsequent experimental evolution in the novel environment, led to successful transitions to selfing and adaptation. Adaptation was not due to the loss of males during transitions, as shown by evolution experiments in exclusively hermaphroditic populations and in male-hermaphrodite populations. Instead, adaptation was due to the displacement of females by hermaphrodites. Genotyping of single-nucleotide polymorphisms further indicated that the observed evolution of selfing rates was not due to selection of standing genetic diversity. Finally, numerical modelling and evolution experiments in male-female populations demonstrate that the improvement of male fitness components may diminish the opportunity for reproductive assurance. Conclusions: Our findings support the hypothesis that reproductive assurance can drive the transition from outcrossing to selfing, and further suggest that the success of transitions to selfing hinges on adaptation of obligate outcrossing populations to the environment where outcrossing was once a limiting factor.

opencc-zeroDec 2013View details →

Data from: Maximally informative foraging by Caenorhabditis elegans

Animals have evolved intricate search strategies to find new sources of food. Here, we analyze a complex food seeking behavior in the nematode Caenorhabditis elegans (C. elegans) to derive a general theory describing different searches. We show that C. elegans, like many other animals, uses a multi-stage search for food, where they initially explore a small area intensively ('local search') before switching to explore a much larger area ('global search'). We demonstrate that these search strategies as well as the transition between them can be quantitatively explained by a maximally informative search strategy, where the searcher seeks to continuously maximize information about the target. Although performing maximally informative search is computationally demanding, we show that a drift-diffusion model can approximate it successfully with just three neurons. Our study reveals how the maximally informative search strategy can be implemented and adopted to different search conditions.

opencc-zeroDec 2014View details →

Data from: Travelling at a slug's pace: possible invertebrate vectors of Caenorhabditis nematodes

Background: How do very small animals with limited long-distance dispersal abilities move between locations, especially if they prefer ephemeral micro-habitats that are only available for short periods of time? The free-living model nematode Caenorhabditis elegans and several congeneric taxa appear to be common in such short-lived environments, for example decomposing fruits or other rotting plant material. Dispersal is usually assumed to depend on animal vectors, yet all current data is based on only a limited number of studies. In our project we performed three comprehensive field surveys on possible invertebrate vectors in North German locations containing populations of C. elegans and two related species, especially C. remanei, and combined these screens with an experimental analysis of persistence in one of the vector taxa. Results: Our field survey revealed that Caenorhabditis nematodes are commonly found in slugs, isopods, and chilopods, but are not present in the remaining taxonomic groups examined. Surprisingly, the nematodes were frequently isolated from the intestines of slugs, even if slugs were not collected in close association with suitable substrates for Caenorhabditis proliferation. This suggests that the nematodes are able to enter the slug intestines and persist for certain periods of time. Our experimental analysis confirmed the ability of C. elegans to invade slug intestines and subsequently be excreted alive with the slug feces, although only for short time periods under laboratory conditions. Conclusions: We conclude that three invertebrate taxonomic groups represent potential vectors of Caenorhabditis nematodes. The nematodes appear to have evolved specific adaptations to enter and persist in the harsh environment of slug intestines, possibly indicating first steps towards a parasitic life-style.

opencc-zeroDec 2015View details →

Data from: Mutation is a sufficient and robust predictor of genetic variation for mitotic spindle traits in Caenorhabditis elegans

Different types of phenotypic traits consistently exhibit different levels of genetic variation in natural populations. There are two potential explanations: either mutation produces genetic variation at different rates, or natural selection removes or promotes genetic variation at different rates. Whether mutation or selection is of greater general importance is a longstanding unresolved question in evolutionary genetics. We report mutational variances (VM) for 19 traits related to the first mitotic cell division in C. elegans, and compare them to the standing genetic variances (VG) for the same suite of traits in a worldwide collection C. elegans. Two robust conclusions emerge. First, the mutational process is highly repeatable: the correlation between VM in two independent sets of mutation accumulation lines is ~0.9. Second, VM for a trait is a good predictor of VG for that trait: the correlation between VM and VG is ~0.9. This result is predicted for a population at mutation-selection balance; it is not predicted if balancing selection plays a primary role in maintaining genetic variation.

opencc-zeroDec 2014View details →

Data from: Rapid evolutionary responses of life history traits to different experimentally-induced pollution in Caenorhabditis elegans

Background Anthropogenic disturbances can lead to intense selection pressures on traits and very rapid evolutionary changes. Evolutionary responses to environmental changes, in turn, reflect changes in the genetic structure of the traits, accompanied by a reduction of evolutionary potential of the populations under selection. Assessing the effects of pollutants on the evolutionary responses and on the genetic structure of populations is thus important to understanding the mechanisms that entail specialization to novel environmental conditions or resistance to novel stressors. Results Using an experimental evolution approach we exposed Caenorhabditis elegans populations to uranium, salt and alternating uranium-salt environments over 22 generations. We analyzed the changes in the average values of life history traits and the consequences at the demographic level in these populations. We also estimated the phenotypic and genetic (co)variance structure of these traits at different generations. Compared to populations in salt, populations in uranium showed a reduction of the stability of their traits structure and a higher capacity to respond by acclimation. However, the evolutionary responses of traits were generally lower for uranium than salt and the evolutionary responses in the alternating uranium-salt environment were between those of constant environments. Consequently, at the end of the experiment, the population rate of increase were higher in uranium than in salt and intermediate in the alternating environment. Conclusions Our multigenerational experiment confirmed that rapid adaptation to different polluted environments may involve different evolutionary responses resulting demographic consequences. These changes are partly explain by the effects of the pollutants on the genetic (co)variance structure of traits and the capacity of acclimation to novel conditions. Finally, our results in the alternating environment may confirm the selection of a generalist type in this environment.

opencc-zeroDec 2015View details →

Data from: The mutational structure of metabolism in Caenorhabditis elegans

A properly functioning organism must maintain metabolic homeostasis. Deleterious mutations degrade organismal function, presumably at least in part via effects on metabolic function. Here we present an initial investigation into the mutational structure of the Caenorhabditis elegans metabolome by means of a mutation accumulation experiment. We find that pool sizes of 29 metabolites vary greatly in their vulnerability to mutation, both in terms of the rate of accumulation of genetic variance (the mutational variance, VM) and the rate of change of the trait mean (the mutational bias, ΔM). Strikingly, some metabolites are much more vulnerable to mutation than any other trait previously studied in the same way. Although we cannot statistically assess the strength of mutational correlations between individual metabolites, principal component analysis provides strong evidence that some metabolite pools are genetically correlated, but also that there is substantial scope for independent evolution of different groups of metabolites. Averaged over mutation accumulation lines, PC3 is positively correlated with relative fitness, but a model in which metabolites are uncorrelated with fitness is nearly as good by Akaike's Information Criterion.

Fig. 7 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 7 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 7 Stemspecies pattern reconstruction. Legend for the cladogram: Black squares indicate the following apomorphies: 1) Glottoid apparatus transformed, sectors of metastegostom not spherically protruding; - median bulb prominent oval; - GP3 shifted posterior of cloaca level (only two precloacal papillae present); - GP7-9 clustered; - spiculum blade dorsally velum-like. 2) GPs 3-6 clustered, but with small gaps in betw een; - GP6 thickened, its tip em bedded w ithin the bursa velum; - posterior part o f bursa velum w ith "wash-board pattern" (transverse striae); - spiculum shaft with transverse seam; - dauerlarvae unsheathed. 3) Stoma triangular in cross section; - spiculum terminally notched or dentated and w ith an oval "w indow " in the blade; - postcloacal sensilla filiform; - shortening o f the fem ale tail. 4) Adult cuticle lateral with 3 longitudinal ridges; - sexual dimorphism in cephalic sensilla: they are lost in the female (not projecting to the exterior); - each sector of metastegostom with a triangular flap projecting into the buccal cavity; - precloacal lip anteriorly framed. 5) Gymnostom extended and stegostom shortened, so that only a remnant of the pharyngeal sleeve is present; - gubernaculum distally forked (only presumed for P. friste)

Fig. 6 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 6 Phylogenetic relationships of Caenorhabditis species and two outgroup species. M aximum -likelihood based tree from RAxML. Bootstrap support values (1000 replicates) were 100 all branches, unless noted otherw ise as numbers on branches. Bayesian Posterior Probabilities were 1 for all branches and are not shown. Coloured boxes indicate supergroups, as defined in [3], Strain names from which protein sequence were derived are noted

Fig. 5 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 5 Comparison of exon counts in single-copy orthologues between C monodelphis sp. n. and C elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes w hich had transcripts with CDS lengths 20% longer (orange) or shorter (black) than C. elegans w ere defined as outliers. Linear regression lines are shown. Inset: Frequency histogram o f log2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts, b Comparison of gene structures o f five orthologous gene pairs. Three gene pairs w ere selected at random and a further tw o w ere selected because they show ed a large divergence in exon count

Fig. 4 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 4 Scanning electron micrographs of Caenorhabditis monodelphis sp. n. a,d Anterior end of fem ale; b,c Anterior end of male; e Female vulva; f.g Lateral field of female and male, respectively; h Female anus and tail; ij Male bursa with genital papillae indicated; k Detail of cloaca region with postcloacal sensillae; I Detail of male spiculum

Fig. 3 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 3 Light microscopic images of Caenorhabditis monodelphis sp. n. a General o verview of a dauer larva; b: Ventral view of fem ale reproductive system; c Detailed ventralview of vulva; d Anterior region of male; e Male tailin ventral view, showing seven ventral (v1-7) and tw o dorsal(ad, pd) genital papillae. The phasmids are not visible in this pl ane; f Male tai lin lateral view; g Detai l o f the spicu le; h Detail of the gubernacu lum s____________________________________________________________________________________________________________________________________________________________________________________________________________________

Fig. 2 Cae o in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 2 Cae o abolts mo ode ph s sp. n., matu e spe matozoa fema e post- ıte e sac, TEM A ovvs=spe m ce s

Fig. 1 in Caenorhabditis monodelphis sp. n.: defining CrossMark the stem morphology and genomics of the genus Caenorhabditis

Fig. 1 Line drawings of Caenorhabditis monodelphis sp. n. a Female, schematic overview, b-i Male, b: Male, lateral; c Anterior end in ventral view; d Tail in lateral view; e Tail in ventral view; f Pharyngeal region; g Gubernaculum in ventral view; h Gubernaculum in lateral view; i Spiculum in ateral view

opencc-by-4.0Jun 2024View details →

Reconstruction of gene regulatory networks for Caenorhabditis elegans using tree-shaped gene expression data

Open the record for dataset details and reuse information.

opencc-by-4.0Jul 2024View details →

Data associated with the Caenorhabditis Genomes Project (caenorhabditis.org)

This repository is to permanently accession data available at <a href="download.caenorhabditis.org">download.caenorhabditis.org</a> so that it can be cited in publications.  To get past Zenodo file number restrictions, the three main directories are available as .zip files: <ul> <li><code>genome_files.zip</code>: Genome assembly and annotation files associated with the v2 caenorhabditis.org release</li> <li><code>transcriptome_files.zip</code>: Transcriptome assembly and annotation files associated with the v2 caenorhabditis.org release</li> <li><code>v1_archive.zip</code>: directory containing an archive of the version 1 release, including genomes, annotations, and many other files</li> </ul> If you plan to use the data in this repository, we would appreciate if you could acknowledge members of Caenorhabditis Genomes Project for access to prepublication data (e.g. "We thank members of the Caenorhabditis Genomes Project for prepublication access to genome and transcriptome data").  For an up-to-date list of manuscripts that have used this resource, please see <a href="https://scholar.google.co.uk/scholar?hl=en&q=%22caenorhabditis+genomes+project%22">https://scholar.google.co.uk/scholar?hl=en&q=%22caenorhabditis+genomes+project%22</a>

Fig. 5 in Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

Fig. 5 Comparison of exon counts in single-copy orthologues between C. monodelphis sp. n. and C. elegans. a Exon counts in 6,174 single-copy orthologous gene pairs. C. monodelphis sp. n. genes which had transcripts with CDS lengths 20% longer (orange) or shorter (black) than C. elegans were defined as outliers. Linear regression lines are shown. Inset: Frequency histogram of log2 ratio of C. monodelphis sp. n. exon counts to C. elegans exon counts. b Comparison of gene structures of five orthologous gene pairs. Three gene pairs were selected at random and a further two were selected because they showed a large divergence in exon count

Fig. 2 in Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

Fig. 2 Caenorhabditis monodelphis sp. n., mature spermatozoa in female post-uterine sac, TEM. Arrows = sperm cells

Fig. 1 in Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

Fig. 1 Line drawings of Caenorhabditis monodelphis sp. n. a Female, schematic overview. b-i Male, b: Male, lateral; c Anterior end in ventral view; d Tail in lateral view; e Tail in ventral view; f Pharyngeal region; g Gubernaculum in ventral view; h Gubernaculum in lateral view; i Spiculum in lateral view

Fig. 4 in Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

Fig. 4 Scanning electron micrographs of Caenorhabditis monodelphis sp. n. a,d Anterior end of female; b,c Anterior end of male; e Female vulva; f,g Lateral field of female and male, respectively; h Female anus and tail; i,j Male bursa with genital papillae indicated; k Detail of cloacal region with postcloacal sensillae; l Detail of male spiculum