The genomic basis of adaptation to virulent pathogens in asexual bdelloid rotifers

Sex is embarrassing for scientists, because it is such an inefficient way to make offspring that simple theory says it should not exist at all. In theory, female animals could pass on their genes twice as effectively by making eggs that hatch into identical clones, rather than letting males contribute 50% of the DNA. An all-female 'asexual' population could grow twice as quickly. With this huge advantage, it is hard to see why nearly all plants and animals keep males around, or spend so much time and energy on sex. This is one of the Big Questions that has puzzled biologists since Darwin.

One leading idea is that clonal populations are driven extinct by diseases. If individuals are genetically identical, a pathogen that evolves to infect one can kill them all. Sex continually shuffles DNA and introduces genetic diversity to the immune system. This helps each new generation to resist the ever-changing pathogens. This idea is called the 'Red Queen' hypothesis (RQH), after a character from Alice in Wonderland who had to run all the time to stay in the same place.

Animal groups that completely abandon sex almost always vanish soon afterwards, but it is not clear if this is due to diseases or something else. We plan to answer this by investigating a strange group of animals that seem to break all the rules. Bdelloid rotifers are tiny aquatic invertebrates that seemingly abandoned sex over 50 million years ago, but are highly successful all over the world, with more than 500 species. They have been called 'an evolutionary scandal' because sex is supposed to be indispensable. Their success is a problem for the RQH, as they are attacked by nasty fungal pathogens that can exterminate populations in just a few weeks. Why haven't they gone extinct?

If the RQH is right, bdelloids must have unusual alternative strategies to cope with diseases. We will investigate two possibilities:

(1) Bdelloids might use previously unknown genetic tricks to shuffle their immune defences. Using genome sequencing technology, we will identify the genes and proteins that protect rotifers from fungal attack. We will ask whether variation in these immunity genes is driven by special processes, like odd forms of sex, or a weird mechanism that lets them pick up DNA from other organisms. Evidence for either idea would support the RQH's prediction that even bdelloid rotifers need to 'run' as fast as they can to keep up with pathogens genetically. If we find no such mechanisms, even for immune genes, it would confirm that bdelloids lack genetic shuffling. In either case, we will gain new insights about how animals resist diseases, and perhaps even find antimicrobials that might be useful against fungi.

(2) Bdelloids' ecology and lifestyle might let them escape from pathogens. Bdelloids thrive in temporary patches of moss and rainwater, and have the unusual ability to survive complete desiccation. They form dust-like particles that can be carried by wind for miles, but the fungi cannot survive this process. Perhaps the rotifers disperse among moss patches so often that the pathogens cannot physically keep up, so that the bdelloids 'run away' by dispersal instead of genetic shuffling. To test this scenario we will track changes in rotifer genotypes in moss over time, and see whether incoming animals are better at resisting diseases. If bdelloids are playing ecological "hide-and-seek" with pathogens, it would again show that special mechanisms are needed to replace sex.

Evidence for one or both possibilities would support the RQH by showing how bdelloids escape disease and extinction. It would solve an 'evolutionary scandal' and help explain why sex is so common. But, if we find that bdelloids are thriving without odd genetic or ecological tricks, it would imply that the threat of disease to long-term clonal lineages has been overstated, which would lead to a substantial rethink about the embarrassing problem of sex.

Media and public: There has been considerable and longstanding public interest in the intriguing lifestyle of bdelloid rotifers (e.g. BBC, New York Times, Telegraph, etc). Diseases, sex and extinction are perennial topics of interest. The proposed work contains all these elements and will be readily communicated to a public audience. The key benefit to the public will be knowledge and understanding of evolutionary biology and the genetic and ecological mechanisms by which organisms cope with disease, via an intriguing example. These ideas may raise awareness about the role of genetic diversity in diseases that affect humans (malaria, HIV, influenza) or agriculture (Panama disease, ash dieback, etc).

Scientific training: The project will provide training and mentoring for the researcher co-I and technician, including skills applicable broadly to future academic or industrial employment. In the past 10 years, over fifteen Masters students have conducted 5-month research projects on bdelloid rotifers with the PI or Co-I, receiving training in molecular biology, field biology, statistical analyses and bioinformatics. At least 12 have progressed to PhDs (UK, Germany, Greece, USA) and 3 into research assistant or technical roles at museums or schools. We anticipate similar interest in conducting projects linked to the present proposal, hence contributing training that advances scientific competitiveness and NERC's mission.

Secondary education: The rotifer-parasite system is easy and cheap to bring into classrooms, but covers important science. The Co-I has led sessions with expert biology teachers to develop practical lesson plans involving rotifers, and has delivered these to students from seven schools in the London area, with a particular focus on girls' schools and academies with a high proportion of disadvantaged and minority students. Feedback from teachers and students is consistently positive e.g. "Thank you so much for spending time with us...I can't wait to have my classes go in search of rotifers!" These workshops would continue through the funding period and can be extended to new regions.

Antimicrobial discovery: It is possible we will discover new antimicrobial peptides or other immune effectors expressed by bdelloids, given their track record in revealing new findings. A particular pressure is discovering new antimicrobial compounds, while minimizing development costs of drugs that cannot individually provide long-term protection, because of the rapid evolution of resistance. New molecules from bdelloids, especially if horizontally acquired, might generate useful leads for eventual control of fungal and even bacterial infections. We are ready to promote any such leads in coordination with the Antimicrobial Research Collaborative (www.imperial.ac.uk/arc/).

Pest management: Bdelloid rotifers and their fungi are not economically important, but their unique properties allow deeper understanding of how recombination, dispersal and selection affect host-parasite systems. This knowledge is relevant to the fate of the asexual Cavendish banana cultivar versus Panama disease (from the same order of fungi as our rotifer pathogens), and to biocontrol of obligately asexual nematodes (Meloidogyne), which are major crop pests and suffer from similar fungal pathogens. Many important agricultural pests are themselves asexual, and agronomists have called for better understanding of how Red Queen dynamics affect the control of those populations (e.g. Hoffman et al. 2008, PRSL-B 275: 2480). In future, our project might suggest novel biocontrol strategies for such pests, for example in relation to the spatiotemporal application of control agents and the effect of pest dispersal.