The Red Queen and the bdelloid rotifers: how to keep up with co-evolving parasites in the long-term absence of sexual reproduction
Lead Research Organisation:
Imperial College London
Department Name: Life Sciences
Abstract
Sex is embarrassing for evolutionary biologists, who have struggled for decades to explain why almost all animals and plants engage in such an inefficient activity. In principle, females could transmit their genes with 100% efficiency by producing identical clonal daughters. Sex, by contrast, reduces a female's genetic stake in each offspring to 50%, with the remainder supplied by a male who shares few of the production costs. Given this twofold disadvantage to sexual females, why aren't all organisms asexual?
One leading idea is that a lack of genetic variation leaves asexual populations vulnerable to diseases. In this view, colourfully named the 'Red Queen hypothesis', parasites and pathogens are constantly evolving to overcome the immune defenses of their hosts. Sexual hosts can fight back with new combinations of defensive genes each generation, allowing them to keep up with parasites in an endless co-evolutionary race. However, asexual hosts have no way to change their outdated defences, and are doomed to be overtaken and exterminated. Consistent with this view, lineages that completely abandon sex almost inevitably go extinct soon after, and evidence suggests that disease plays a role. However, there is one remarkable and informative exception.
Bdelloid rotifers are microscopic freshwater invertebrates that abandoned sex and males more than 30 million years ago, but have persisted and diversified into more than 450 species. Their success has been called 'an evolutionary scandal,' because sex was believed to be indispensable. They appear to refute the Red Queen hypothesis, as they suffer from a range of deadly fungal parasites, but have not been driven extinct as predicted. Should we abandon this otherwise promising hypothesis? What if bdelloid rotifers have found unusual alternative ways of dealing with parasites? If so, their asexuality may actually strengthen, rather than challenge the Red Queen hypothesis.
I am investigating whether unique aspects of the bdelloids' lifestyle help them stay ahead of parasites without needing sex. These animals can tolerate complete desiccation, allowing them to thrive in tiny, ephemeral patches of moss and rainwater. When dry, they form miniscule particles that can be transported by wind for hundreds of metres. Crucially, however, their parasitic fungi cannot withstand this process. In principle, therefore, a bdelloid clone could leave its co-adapted parasites behind, and disperse to a new habitat patch where the local parasites are less well-adapted. If these migrations happen often enough, parasites in any patch will be exposed to a constantly changing array of host genotypes, just as if the bdelloids were having sex.
I aim to test this intriguing scenario directly. I will use genetic 'barcodes' to identify and track bdelloid clones as they migrate among patches of moss in UK woodland. I will test whether bdelloids from the same area differ in their resistance to fungal parasites, and determine whether the rotifers or their enemies are 'ahead' in the race. I will set up sterile, elevated patches of moss in the field, to see how quickly they are colonised by windblown bdelloid clones. Some of these new patches will be seeded with parasites, to determine whether their presence favours rotifers with specific genetic immunities. Results will be compared with theoretical work that describes the patterns to expect if bdelloids are indeed playing an ecological game of "hide-and-seek" with their parasites.
If confirmed, this would be a fascinating and unprecedented solution to a universal problem, throwing new light on the role of dispersal in co-evolutionary dynamics. It would also reconcile the 'scandalous' bdelloid rotifers with the Red Queen hypothesis. Alternatively, if this promising scenario is refuted, the bdelloids' success would become even more mysterious and intriguing, forcing a serious reconsideration of the supposed vulnerability of asexuals to parasitism.
One leading idea is that a lack of genetic variation leaves asexual populations vulnerable to diseases. In this view, colourfully named the 'Red Queen hypothesis', parasites and pathogens are constantly evolving to overcome the immune defenses of their hosts. Sexual hosts can fight back with new combinations of defensive genes each generation, allowing them to keep up with parasites in an endless co-evolutionary race. However, asexual hosts have no way to change their outdated defences, and are doomed to be overtaken and exterminated. Consistent with this view, lineages that completely abandon sex almost inevitably go extinct soon after, and evidence suggests that disease plays a role. However, there is one remarkable and informative exception.
Bdelloid rotifers are microscopic freshwater invertebrates that abandoned sex and males more than 30 million years ago, but have persisted and diversified into more than 450 species. Their success has been called 'an evolutionary scandal,' because sex was believed to be indispensable. They appear to refute the Red Queen hypothesis, as they suffer from a range of deadly fungal parasites, but have not been driven extinct as predicted. Should we abandon this otherwise promising hypothesis? What if bdelloid rotifers have found unusual alternative ways of dealing with parasites? If so, their asexuality may actually strengthen, rather than challenge the Red Queen hypothesis.
I am investigating whether unique aspects of the bdelloids' lifestyle help them stay ahead of parasites without needing sex. These animals can tolerate complete desiccation, allowing them to thrive in tiny, ephemeral patches of moss and rainwater. When dry, they form miniscule particles that can be transported by wind for hundreds of metres. Crucially, however, their parasitic fungi cannot withstand this process. In principle, therefore, a bdelloid clone could leave its co-adapted parasites behind, and disperse to a new habitat patch where the local parasites are less well-adapted. If these migrations happen often enough, parasites in any patch will be exposed to a constantly changing array of host genotypes, just as if the bdelloids were having sex.
I aim to test this intriguing scenario directly. I will use genetic 'barcodes' to identify and track bdelloid clones as they migrate among patches of moss in UK woodland. I will test whether bdelloids from the same area differ in their resistance to fungal parasites, and determine whether the rotifers or their enemies are 'ahead' in the race. I will set up sterile, elevated patches of moss in the field, to see how quickly they are colonised by windblown bdelloid clones. Some of these new patches will be seeded with parasites, to determine whether their presence favours rotifers with specific genetic immunities. Results will be compared with theoretical work that describes the patterns to expect if bdelloids are indeed playing an ecological game of "hide-and-seek" with their parasites.
If confirmed, this would be a fascinating and unprecedented solution to a universal problem, throwing new light on the role of dispersal in co-evolutionary dynamics. It would also reconcile the 'scandalous' bdelloid rotifers with the Red Queen hypothesis. Alternatively, if this promising scenario is refuted, the bdelloids' success would become even more mysterious and intriguing, forcing a serious reconsideration of the supposed vulnerability of asexuals to parasitism.
Planned Impact
Beneficiaries include:
Academics & Research Council: The project targets a long-standing problem in evolutionary biology, and involves an unusual group of organisms that generate high-profile interest among geneticists, physiologists, zoologists, limnologists, etc. Data will have value to theoretical and applied ecologists interested in processes driving spatial and temporal diversity. Isolates, specimens and sequences will be useful to taxonomists and molecular ecologists. The prime impact is thus to generate knowledge and understanding, as described in the previous section. The project addresses NERC's mission "to promote and support...high-quality basic research...in terrestrial biology" and "to advance knowledge...and to provide trained scientists that meet the needs of users and beneficiaries".
Higher Education: In the USA, I supervised 8 undergraduate and thesis-level research students over 4 years, training them to use the bdelloid-parasite system. I have worked with 3 UK Masters students since my return. Students learned and applied techniques including microscopy, aseptic culturing, DNA extraction, statistics, etc., in the context of a real biological problem. They generated data which were subsequently published, either as theses or as part of peer-reviewed papers (e.g. Wilson 2011, Biol. J. Linn. Soc. 104: 564). Young scientists seem enthusiastic about the system (e.g. 12 MSc students have conducted 5-month projects on bdelloids at Silwood in the past 7 years, 3 involving parasites). I anticipate similar interest in projects linked to this proposal, and I am happy to contribute training that will advance their scientific competitiveness. I am especially keen to help students improve their scientific writing; teaching this highly transferable skill was my special focus at Cornell.
Pest management: Bdelloids and their fungi are not economically important, but their unique characteristics reveal fundamental properties of host-parasite evolution, especially the relative roles of recombination and dispersal in resistance to parasites. The concepts in this project have significance for pest managers wishing to protect monocultured or clonal host species, or control asexual crop pests biologically. Potential impact in these areas will be realised by communicating results at topical meetings of mycologists and crop scientists, who can then apply the insights to target systems.
Public understanding of science: There has been considerable public interest in the evolution of sex, parasites and the weird lifestyle of bdelloid rotifers. The proposed work contains all of these elements, and will make an excellent vehicle to increase public knowledge and understanding of evolutionary biology, ecological dynamics, and microscopic biodiversity. I communicated my early results in 2010 to a US and global audience via national radio, podcasts and online videos, and major newspapers and magazines in over 14 languages. However, the story was not picked up extensively by the UK media at the time, so the UK public will hear about the work at an even more exciting stage, as more definitive results come in from the currently proposed project.
Secondary education: In 2010, I was involved in the Cornell University Institute for Biology Teachers, which forges links between active researchers and schools. I introduced the bdelloid-parasite system to teachers, and during subsequent workshops we developed plans to use these organisms in practical lessons. Bdelloids and parasites are found everywhere, and can be studied with little more than a student microscope and agar dishes. Feedback confirms that students and teachers alike were fascinated to discover the lethal, alien drama that plays out beneath their feet. By replicating and extending this outreach to receptive schools in the UK, I will offer biology teachers an accessible, exciting system in which to demonstrate principles of microscopy, ecology, parasitism and taxonomy.
Academics & Research Council: The project targets a long-standing problem in evolutionary biology, and involves an unusual group of organisms that generate high-profile interest among geneticists, physiologists, zoologists, limnologists, etc. Data will have value to theoretical and applied ecologists interested in processes driving spatial and temporal diversity. Isolates, specimens and sequences will be useful to taxonomists and molecular ecologists. The prime impact is thus to generate knowledge and understanding, as described in the previous section. The project addresses NERC's mission "to promote and support...high-quality basic research...in terrestrial biology" and "to advance knowledge...and to provide trained scientists that meet the needs of users and beneficiaries".
Higher Education: In the USA, I supervised 8 undergraduate and thesis-level research students over 4 years, training them to use the bdelloid-parasite system. I have worked with 3 UK Masters students since my return. Students learned and applied techniques including microscopy, aseptic culturing, DNA extraction, statistics, etc., in the context of a real biological problem. They generated data which were subsequently published, either as theses or as part of peer-reviewed papers (e.g. Wilson 2011, Biol. J. Linn. Soc. 104: 564). Young scientists seem enthusiastic about the system (e.g. 12 MSc students have conducted 5-month projects on bdelloids at Silwood in the past 7 years, 3 involving parasites). I anticipate similar interest in projects linked to this proposal, and I am happy to contribute training that will advance their scientific competitiveness. I am especially keen to help students improve their scientific writing; teaching this highly transferable skill was my special focus at Cornell.
Pest management: Bdelloids and their fungi are not economically important, but their unique characteristics reveal fundamental properties of host-parasite evolution, especially the relative roles of recombination and dispersal in resistance to parasites. The concepts in this project have significance for pest managers wishing to protect monocultured or clonal host species, or control asexual crop pests biologically. Potential impact in these areas will be realised by communicating results at topical meetings of mycologists and crop scientists, who can then apply the insights to target systems.
Public understanding of science: There has been considerable public interest in the evolution of sex, parasites and the weird lifestyle of bdelloid rotifers. The proposed work contains all of these elements, and will make an excellent vehicle to increase public knowledge and understanding of evolutionary biology, ecological dynamics, and microscopic biodiversity. I communicated my early results in 2010 to a US and global audience via national radio, podcasts and online videos, and major newspapers and magazines in over 14 languages. However, the story was not picked up extensively by the UK media at the time, so the UK public will hear about the work at an even more exciting stage, as more definitive results come in from the currently proposed project.
Secondary education: In 2010, I was involved in the Cornell University Institute for Biology Teachers, which forges links between active researchers and schools. I introduced the bdelloid-parasite system to teachers, and during subsequent workshops we developed plans to use these organisms in practical lessons. Bdelloids and parasites are found everywhere, and can be studied with little more than a student microscope and agar dishes. Feedback confirms that students and teachers alike were fascinated to discover the lethal, alien drama that plays out beneath their feet. By replicating and extending this outreach to receptive schools in the UK, I will offer biology teachers an accessible, exciting system in which to demonstrate principles of microscopy, ecology, parasitism and taxonomy.
People |
ORCID iD |
| Christopher Wilson (Principal Investigator / Fellow) |
Publications
Nowell RW
(2018)
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species.
in PLoS biology
Pathak A
(2020)
Comparative genomics of Alexander Fleming's original Penicillium isolate (IMI 15378) reveals sequence divergence of penicillin synthesis genes.
in Scientific reports
Wilson C
(2013)
Spatial and temporal escape from fungal parasitism in natural communities of anciently asexual bdelloid rotifers
in Proceedings of the Royal Society B: Biological Sciences
Wilson CG
(2018)
Cross-Contamination Explains "Inter and Intraspecific Horizontal Genetic Transfers" between Asexual Bdelloid Rotifers.
in Current biology : CB
| Description | Bdelloid rotifers are microscopic animals that live in almost every pond, puddle and patch of moss in the world. Over 400 species have been described, and millions of individuals examined, but surprisingly, all are female. Apparently, males have not existed for millions of years; the females lay unfertilised eggs that hatch into identical asexual daughters. Their success puzzles biologists, because asexual groups are thought to lack the genetic variation needed to diversify and adapt to changing conditions. This award has enabled me and my collaborators to understand how these unusual animals have persisted in the face of ever-changing threats, especially infectious diseases. The results of our fieldwork and genetic sequencing have shed light on the role of variation in responding to environmental change, the relationship between hosts and parasites, and one of the Big Questions in biology: the purpose of sexual reproduction itself. We have shown that bdelloid rotifers have been coevolving with virulent fungal parasites for approximately 50 million years despite their lack of sex. We reconstructed the evolutionary relationships of fungi that attack bdelloids, dated using a fossil from amber. One group, Rotiferophthora, is 46.2 million years old. Using experimental cross-inoculations and infectivity modelling, we demonstrated that Rotiferophthora and bdelloids have been reciprocally coevolving. Because rotifers are transparent, we could even see the infection and resistance mechanisms at work inside their bodies. Our finding of ancient and sustained resistance to fungi seems to challenge the hypothesis that males and sex are required to keep up in an evolutionary race with lethal pathogens. We suggest that bdelloids are dealing with pathogens using unusual genetic and ecological mechanisms, which we went on to investigate. The work achieved two further aims. Because obligate parasites cannot have diversified before their hosts, our work established a new minimum age for bdelloid rotifers as an asexual group, pre-dating previous estimates by 25 million years. We also developed a new lab model for fungal disease in animals, with advantages including clonal reproduction, long-term frozen storage, and direct visualisation of immune responses. In field experiments, we found that wild rotifer populations commonly escape from fungal epidemics by drying up and blowing away. When their habitats desiccate, the rotifers survive by entering a dormant state, and are blown like dust on the wind to colonise new habitats. However, their fungal parasites cannot survive or travel without water, and are destroyed. We used direct trapping to show that wind-blown rotifers migrate rapidly: a genetically diverse immigrant community can be established within just three weeks. This result supports a theoretical model suggesting that asexual populations can persist if they rapidly escape changing diseases in space and time. If so, bdelloid rotifers may actually be an exception that proves the rule: they avoid diseases in a different way from sexual organisms. We also reconstructed relationships for other major fungal parasites of rotifers, revealing six independent origins of parasitism. Many arose in fungal groups that usually attack other hosts, including plants and nematodes. This suggests that animals without sex may be quite vulnerable to acquiring new diseases, even from distantly related hosts, and that ecological opportunity is a key factor in pathogen host shifts. The data also help fill evolutionary gaps in the relationships of economically important pathogenic fungi that attack plants or insects. Other outputs include the discovery of six new species, two new genera and one new family. I collaborated with Polish researchers to identify fungal predators destroying beneficial rotifers in commercial wastewater treatment plants. We also discovered an unusual mechanism of disease resistance, in which asexual rotifers infected with a fungus sometimes spontaneously die in order to prevent the fungus from reproducing and killing their whole population. This mechanism has been described in bacteria before, but not in animals. In sum, the work has helped test and update current thinking about the long-term effects of genetic diversity on adaptation to disease. It supports the view that sexual reproduction facilitates long-term coevolution with parasites and pathogens, but reveals that other ecological strategies also can help compensate for lack of genetic diversity. It has shed new light on the diversity and host range of pathogenic fungi. Other outputs include two critical revisions of previously suggested models of genome evolution in the animals studied. |
| Exploitation Route | One key outcome is a new experimental system that combines an under-studied class of pathogens (fungi) with a historically under-studied group of animals (Spiralians). The bdelloid-Rotiferophthora system is highly tractable and well characterised phylogenetically and phenotypically. It is now available for work on the evolution, ecology, physiology and molecular biology of immunity. Workers in Belgium, Germany and Poland are already following up on our results. The key question we now opened up for investigation is whether bdelloid rotifers show exotic genetic mechanisms that compensate for their lack of sex by generating immunological diversity. We have begun to investigate this, and have so far demonstrated that evolution of resistance does not occur on rapid timescales, nor does extended or repeated desiccation change the genetic propensity to resist pathogens. A future focus is the interaction of bdelloid rotifers with bacteria, as pathogens, prey and competitors. The fact that bdelloids are capable of coevolution across macroevolutionary timescales raises some exciting hypotheses about potential interactions with bacteria, and we have developed a cell line and monoxenic rotifer culture resources to take this forward,. Our main result highlights an oblique technique for establishing the age of important groups that do not fossilize well. We were able to establish a robust age for bdelloid rotifers by relying on molecular dating of their obligate parasites. We hope this will guide similar approaches in other groups. Our findings are already being used by applied researchers in Poland to improve the control of fungi that destroy rotifers in commercial wastewater treatment plants. I am collaborating with a group focusing on interactions between oomycete pathogens and C. elegans, to further investigate the genetic basis of fungal resistance in rotifers. Our fungal sequence data and culture materials will certainly be used in future by anyone studying the evolution of economically important biocontrol and plant-pathogenic fungal pathogens in the order Hypocreales. |
| Sectors | Agriculture, Food and Drink,Education,Environment,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology |
| URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_11-7-2013-12-50-10 |
| Description | Scientific training: The grant helped provide training and laboratory experience to fourteen postgraduate students, four undergraduates and one Key Stage 4 work-experience student, from the UK and EU. The Masters students helped generate data (described in Key Findings) that form part of upcoming publications, which will help them compete for jobs in the academic or private sectors. Five have already been co-authors of published conference abstracts, nine have secured PhDs and three are working in the private sector. Secondary education: In accordance with my Pathways to Impact plan, I worked with a corporate partner (Exscitec, Ltd) to develop and deliver a STEM-related activity to over 100 students from six schools and academies around Inner London. The focus has been on schools from historically disadvantaged areas, and those with female students, to help foster a diverse representation among future scientists. I have been introducing students in Key Stages 3 and 4 to principles of genetics, evolution and microscopy via the rotifer research funded by this award. These activities helped increase interest in STEM careers and biological sciences among traditionally under-represented groups. Feedback was collected from students who participated in the workshops and was very positive. I have subsequently returned to one of the Exscitec partner schools five times to help with preparation of STEM students for higher education. The students I mentored went on to secure places studying STEM topics, including at Oxbridge. Public engagement: My work has been featured in a book (http://www.bloomsbury.com/uk/sex-on-earth-9781408193419/), blogs, social media and twice on BBC Radio 4 (https://www.bbc.co.uk/programmes/b09sn980). I have used my findings to update publicly available knowledge repositories such as Wikipedia. I have organised several public outreach events around this research theme, including an evening on the topic of sexuality at the Science Museum, and microscopy activities for the general public at several open days. I have presented elements of the work during an innovative outdoor public walking event focused on evolutionary biology- the Ancestor's Trail. Commercial Wastewater Management As part of this award, I have collaborated with researchers in Poland to characterise fungal pests that interfere with commercial wastewater processing by killing rotifers that provide debulking services. This collaboration included a two week Polish-funded placement in my lab for a visiting researcher, promoting cross-EU knowledge exchange. The results obtained from our collaboration are being used to identify problematic fungi in Polish wastewater treatment plants, and the relevant organisms have been isolated and catalogued in culture collections for the first time. |
| Sector | Creative Economy,Education,Environment,Culture, Heritage, Museums and Collections |
| Impact Types | Cultural,Societal,Economic |
| Description | research culture |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | PI participated in two consultation and focus-group events for Early Career Researchers, hosted at the Royal Society in 2016 and 2017. For outputs, see the recent Royal Society report: Research culture: embedding inclusive excellence (2018). This document will have broad impact in terms of policy and practice relating to UK scientific research culture over the next 15 years. |
| URL | https://royalsociety.org/~/media/policy/Publications/2018/research-culture-workshop-report.pdf |
| Description | NERC Standard Grant |
| Amount | £523,567 (GBP) |
| Funding ID | NE/S010866/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2022 |
| Title | Axenic rotifers |
| Description | We have developed a protocol to dissociate cultured lines of bdelloid rotifers from their co-cultured bacterial community and generate axenic individuals. We have also isolated a bacterial cell line that supplies sufficient nutrients to sustain growth and reproduction of rotifers in the absence of any other organism (a monoxenic system). |
| Type Of Material | Cell line |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Control over the bacterial community greatly increases the power and repeatability of experiments with bdelloid rotifer lines, and opens the door to investigating the coevolutionary relationships between these animals and pathogenic bacteria. It brings the system a step closer to the level of control and precision seen in work with the nematode model C. elegans. |
| Title | R_silwoodensis |
| Description | I have isolated and determined how to rapidly culture a new species of bdelloid rotifer belonging to a genus that is the focus of particular study in our field. This is important because members of this genus are rarely amenable to laboratory culture, and this clonal line extends the range of questions we can ask about the unusual genome structure found in the group. This will be described as a new species, and is already available to share with other groups around the world. Its genome is currently being sequenced. |
| Type Of Material | Biological samples |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | None yet, but sequencing is in progress. The resulting genome assemblies ought to be of high quality, as we have been able to use the most advanced long-read methods thanks to the ability to extract DNA from large numbers of uniform clonal animals in laboratory culture. |
| Title | ZCAR |
| Description | Five PCR primers were developed to amplify a conserved nuclear protein-coding marker in bdelloid rotifer genomes (a zinc-carboxypeptidase gene, ZCAR). This marker is also exon-primed, intron-crossing (EPIC), which increases the power to detect variation and phase two homologous alleles. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | This marker has been sequenced for over 30 isolates and the results form part of our aligned sequence matrix. This has been shared with collaborators and used to reconstruct the phylogenetic history of the Class Bdelloidea. |
| Title | arsef |
| Description | I have submitted over 50 fungal culture isolates from the UK to the United States Department of Agriculture, for the Agricultural Research Service collection of Entomopathogenic Fungi (ARSEF). These isolates are now available for use by other researchers in the areas of soil and pest science. |
| Type Of Material | Biological samples |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | Several under-represented fungal groups are now available in culture for the first time, including new families, genera and species. These cultures will be referenced in all publications arising from this award, and are now available to other groups for future work on this new host-parasite system. |
| URL | http://www.ars.usda.gov/News/docs.htm?docid=12125 |
| Title | bioassay |
| Description | We have developed a new, standardised assay to quantify the infectivity of fungal pathogens against bdelloid rotifers, and applied this method to quantify hundreds of host-pathogen interactions. |
| Type Of Material | Physiological assessment or outcome measure |
| Year Produced | 2013 |
| Provided To Others? | Yes |
| Impact | This quantitative assay forms the basis of most of the published outputs of this project, and is already being used in follow-up projects, looking at the experimental evolution of pathogen resistance in asexuals and other topics in disease ecology. |
| Title | rotifer cultures |
| Description | As part of this project and its goals, I have isolated and cultured approximately clonal 30 lines of bdelloid rotifers, and made long-term frozen archives of these isolates for future use. I have shared some of these lines with other groups pursuing genetic and genomic studies in this and other systems. |
| Type Of Material | Biological samples |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | There were previously only a very limited number of reference clones of bdelloid rotifers broadly available for research, and many of the research groups that previously maintained these have since become inactive. This is, to our knowledge, the largest collection of living bdelloid isolates in the world, and we will continue to make them available for future research. |
| Title | ConTAMPR |
| Description | ConTAMPR is a method developed by the PI to detect minority DNA sequences in the fluorescence chromatogram traces for Sanger-sequenced PCR products, and to test statistically whether these minority sequences match a particular reference sequence. It stands for Contingency Table Analysis of Minority Peak Ranks. After experimentally validating this technique on deliberately contaminated samples, the PI and co-authors applied it to identify extensive cross-contamination in the data supporting a 2016 paper in the widely-read journal Current Biology, revealing that the data and findings in that publication are not reliable. The method has broad potential to identify contamination in other Sanger-sequenced legacy DNA datasets, and might help revive the practice of uploading original sequencing chromatograms to public repositories as part of the data transparency movement. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | After the publication of the method as part of an open-access pre-print, our colleagues at the University of Namur developed a software implementation of the technique that will greatly increase the utility and speed of the method. They have made this implementation openly available via GitHub (https://github.com/jnarayan81/autoConTAMPR), and have independently reproduced our results demonstrating extensive DNA cross-contamination in a 2016 dataset (https://doi.org/10.1101/368209). |
| URL | https://data.mendeley.com/datasets/fsjpwrnv4t/1 |
| Title | Cross-inoculation dataset |
| Description | This dataset records the responses of various rotifer clones to inoculation with different isolates of the fungal pathogen Rotiferophthora, at multiple timepoints. It has over 3500 entries, each representing approximately 10 animals over 72 hours. The conditions for each experimental exposure are also recorded, along with the provenance of the host and parasite isolates. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | No |
| Impact | This dataset is the second major output of the award, and will form the basis for several publications. It will be made publicly available via DRYAD as soon as the first paper is published. The data will support the future use of bdelloid rotifers as a new model host-parasite system for investigating genetic diversity, immunity and coevolution. |
| Title | Dispersal data |
| Description | As part of the primary project goals, natural habitat patches have been tracked over multiple years (2015-2018) using intensive sampling and genetic barcoding methods, to measure dispersal rates and clonal diversity in bdelloid rotifers. A dataset has been obtained, comprising mitochondrial genetic barcodes for over 1000 animals, and revealing patterns of diversity, local adaptation and dispersal, as set out in the project goals. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | No |
| Impact | The estimates of dispersal rates obtained from this dataset have been shared with other groups, and are informing analysis of other genetic and ecologial data. The full dataset will be published as part of a paper on dispersal. The data were important in establishing feasibility parameters for a subsequent successful NERC grant: NE/S010866/1. |
| Title | Hypocrealean sequences |
| Description | An alignment of concatenated DNA sequences for six loci representing approximately 200 fungal pathogens in the Order Hypocreales, with a focus on newly generated sequences for parasites of rotifers. Over 200 novel sequences have been generated as a result of this project, all from species for which no molecular data was previously available. The data have been analysed to produce novel phylogenies for Hypocreales, which form part of this research database. |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | This dataset will form the basis for multiple publications arising from the award. It will be released publicly via GenBank and TreeBASE once the first major paper is published. |
| Title | Phylogenetic matrix |
| Description | An alignment of new sequences generated from approximately 20 bdelloid rotifer clones cultured as part of the project, along with related sequences from other projects. This includes sequences for new phylogenetic markers developed as part of the project, along with standard barcode markers. The data have been analysed to produce a broad draft phylogeny of the Class Bdelloidea, which has not previously been available, accomplishing one of the project goals. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | No |
| Impact | This part of the project has been shared with experts in bdelloid taxonomy and phylogeography in the UK, Italy and the Czech Republic. It is informing revisions of the taxonomy of the broad group, and is also being used to guide current genomic research in this system, funded as part of other projects. The data and phylogenies will be shared publicly when the output from this project is published. |
| Title | Predator sequences |
| Description | As part of the collaboration with researchers in Poland, we generated genetic data for predators of rotifers found in wastewater treatment plants. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | The genetic data have enabled the Polish group to identify fungi that are inhibiting the efficient treatment of wastewater, and to monitor their diversity and prevalence in an objective way across multiple sites. |
| Description | Cator-Russell Mosquito collaboration |
| Organisation | Imperial College London |
| Department | Department of Life Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I provided expertise in microscopy and the culturing of microinvertebrates and protists to colleagues at Imperial College who were investigating copepod predation on mosquito larvae, as part of a biological control study. |
| Collaborator Contribution | My colleagues cultured larvae of the invasive Asian tiger mosquito (Aedes albopictus) under controlled conditions and exposed them to predation by copepods. They characterised the functional response of the predators and established that they would be potentially suitable biocontrol agents against populations of mosquitoes. The research has potential impact and relevance to disease control and global health under climate change. |
| Impact | Manuscript: " Size, not temperature, drives cyclopoid copepod predation of invasive mosquito larvae " https://www.biorxiv.org/content/10.1101/839480v2 |
| Start Year | 2018 |
| Description | Faust- Malaria coevolution |
| Organisation | University of Arizona |
| Department | Ecology and Evolutionary Biology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | I am providing expertise in phylogenetics and coevolutionary theory for a project investigating the historical dynamics of host switching in primate malarias. |
| Collaborator Contribution | My partners are providing new data on the distribution of malarial parasites in primates, along with new molecular data for the genus Plasmodium. |
| Impact | The collaboration is multidisciplinary, involving ecology, parasitology, evolutionary biology, epidemiology and public health. |
| Start Year | 2015 |
| Description | Namur |
| Organisation | University of Namur |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | We have provided advice and training on the ecology and culturing of bdelloid rotifers, and their parasites, including two trips to Namur to identify appropriate sites for sampling and to discuss methods and results. We have corresponded extensively with our partners in Belgium to help resolve important uncertainties in one of their recent publications, providing genomic and methodological advice. |
| Collaborator Contribution | Our partners have provided genetic sequences, primer sequences and animal samples for use in our disease characterisation studies. They sent a Masters student to assist in our group for several months and learn relevant techniques, and they have shared genetic data of importance in resolving significant mistakes in published literature. The Namur group have recently provided a software implementation of a new method (ConTAMPR) that PI Chris Wilson developed to test for DNA contamination in Sanger chromatograms, and they have made it publicly available to apply to other datasets. |
| Impact | The collaboration combines evolutionary biology, genetics, genomics and ecology. It has helped maintain international links, and the same Belgian partners are now providing input on another NERC-funded project (NE/M01651X/1). |
| Start Year | 2013 |
| Description | TGB RWN |
| Organisation | Imperial College London |
| Department | Department of Electrical and Electronic Engineering |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | I provided training, supervision, logistical and methodological resources for a technician and postdoc conducting work on a related project (NE/M01651X/1) involving the same experimental system (bdelloid rotifers). I provided assistance with analysis and interpretation of genomic data, experimental validation of genome assemblies using Sanger sequencing, editing and data contributions to a paper now published in PLoS Biology. I initiated and coordinated a separate study now published in Current Biology, with my collaborators as co-authors. I undertook collections of animals from nature and developed new methods for culturing them, which have extended the original scope of the project. I have also extracted and amplified high quality genomic DNA for over 50 animals and am now collaborating on interpreting data for further papers. |
| Collaborator Contribution | The collaborating partners have provided genomic and transcriptomic data and extensive bioinformatic expertise enabling us to achieve a shared project goal of building a well-supported phylogeny for bdelloid rotifers as well as assembling new genomes from multiple families. We are now approaching questions of adaptation and genome architecture. They have also provided analytical expertise in Bayesian phylogenetic and statistical packages, which has greatly increased the utility of data collected during my project. |
| Impact | A publication in PLoS Biology (https://doi.org/10.1371/journal.pbio.2004830), leading to a substantial revision of the theoretical landscape surrounding DNA repair and horizontal gene transfer in bdelloid rotifers. Another publication in Current Biology (https://doi.org/10.1016/j.cub.2018.05.070) that resolves earlier uncertainties about an extraordinary pattern of non-canonical gene transfer. Technician training; phylogenetic and molecular datasets; statistical models and generalised code for co-phylogenetic analysis of infectivity data. Further funding has been raised to support and extend this collaboration in the form of a major grant awarded jointly (NE/S010866/1). |
| Start Year | 2015 |
| Description | Wastewater treatment- Institute of Environmental Sciences, Krakow |
| Organisation | Jagiellonian University |
| Country | Poland |
| Sector | Academic/University |
| PI Contribution | I provided training, advice and data for a senior researcher from Jagiellonian University, who visited Imperial College for two weeks in 2015 to observe and assist with ongoing work in my laboratory. I provided access to equipment, including high-quality cameras and microscopes, and molecular sequencing techniques. I also helped identify pathogens of rotifers isolated from commercial wastewater treatment plants in Poland, where they have been decreasing the efficiency of sludge debulking processes. |
| Collaborator Contribution | My partners from Krakow contributed ten cultures of rotifers collected from Polish wastewater treatment plants, along with associated cultures of fungal predators, many of which are undescribed. They showed me several useful techniques in culturing monogonont rotifers, and they brought me a supply of a proprietary food formula. My visitor also conducted many hours of work in my laboratory, isolating and subculturing the rotifers and pathogens for molecular identification and formal description. |
| Impact | Ongoing collaboration in both directions. Published outputs not yet available, but societal impact has already been partially realised through the researcher exchange, via improved knowledge sharing and international collaboration. The main outputs are genetic data (already obtained) and a paper (currently in preparation) describing and characterising multiple new species of fungal predators of rotifers in wastewater treatment plants. Another output is five freely available live cultures of the relevant fungi, deposited with the USDA-ARS collection of entomopathogenic fungi for future research. In the longer term, the collaboration will yield economic impact by helping my Polish colleagues improve the process of wastewater treatment using rotifers in activated sludge. |
| Start Year | 2015 |
| Description | Ancestor's Trail |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Inspired by Richard Dawkins' book, The Ancestor's Tale, this annual outdoor event features scientists and members of the public walking together along routes representing the tree of life in reverse, starting at points that represent different extant groups in the present day and symbolically travelling back in time to the last common ancestor. At points along the way and at the end, researchers present elements of their work to the participants. In this case, I gave an impromptu public talk about the work supported by this award to about 30-40 people in a pub at the end of the trail, took questions and engaged in follow-up conversations both there and along the route. Participants showed interest in the work, requested more details, asked for advice about amateur microscopy, and some participants took videos that were shared on social media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://ancestorstrail.org.uk/background |
| Description | Bugs! |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Several hundred members of the general public attended an open day at the Silwood Park campus, where I presented two interactive stands. One was on the evolution of warning colouration, aimed at children from 6-12, and the other was called "Fantastic Minibeasts", and was aimed at a general audience, introducing them to microscopic invertebrates, including rotifers, nematodes and tardigrades. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/eventssummary/event_4-6-2015-10-11-47 |
| Description | Bugs2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Several hundred members of the general public attended an open day at the Silwood Park campus, where I presented an interactive stands called "Fantastic Minibeasts", aimed at introducing a general audience (and especially children) to microscopy and microscopic invertebrates, including rotifers, nematodes and tardigrades. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/naturalsciences/silwoodparkcampus/even... |
| Description | Dawkins |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | One of my papers was reported in a Twitter message by the prominent evolutionary biologist Richard Dawkins, who has over 2 million followers. This led to dozens of retweets and comments, which helped spread the important message to a global audience, including members of the public who are interested in biology even if not active in research. One of the key themes of the Twitter discussion was the recognition that the scientific process occasionally gets things wrong, but others can then correct those mistakes with further careful work. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://twitter.com/RichardDawkins/status/1017767236923199489 |
| Description | Habitats and Adaptation at Upton |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | I attended a Primary school in Kent (Upton Junior School) as a guest speaker to present a two-hour interactive lesson about adaptations, as part of a curriculum module on animals and habitats. I spoke to 30 children, we played some games to simulate natural selection, and I interacted with several teachers, providing a lesson plan for future years. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Life Without Sex Science Museum Late |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | I attended a large event at the Science Museum in London, as part of their 'Lates' series. The topic was 'Sexuality', and I presented a hands-on stand with live microscope feeds and cultures of rotifers and fungus. The event lasted for 4 hours and was extremely well attended; I introduced well over a hundred members of the public to rotifers, and to ideas about genetic diversity and evolutionary biology. Audience members from whom I requested feedback reported an improved understanding of the importance of genetic diversity in resisting disease, and the principles of natural selection. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.sciencemuseum.org.uk/visitmuseum/plan_your_visit/lates |
| Description | RWNBlog |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A collaborator was invited to post an extended entry as a guest at a popular genomics blog, describing two pieces of collaborative research we conducted jointly. This raised awareness of the important new results within the community of researchers and a broader readership. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://nematodes.org/blog/the-case-of-the-scandalous-bdelloids-part-1/ |
| Description | Reaching Further: London School Outreach Workshop 'Invisible Animals' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | Yes |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | I worked with science teachers from three schools in the London area, and a corporate partner, Exscitec, to develop and deliver an educational workshop activity for students in Years 7-8, themed around my research. The workshop focused on skills in microscopy, and knowledge of scale, microbiology and biodiversity. I brought this hands-on STEM activity to nearly 100 students from five schools in disadvantaged areas of London, as part of broader STEM open days organised by Exscitec. Feedback from the students and teachers was extremely positive. Outreach facilitators and London schoolteachers at the initial workshop expressed great enthusiasm for a microscopy activity I have been planning, and are now helping me develop it into a curriculum-linked engagement session in schools. I have developed printable materials and instructions to accompany this activity. |
| Year(s) Of Engagement Activity | 2014,2015,2016 |
| URL | http://www3.imperial.ac.uk/outreach/wohlreachoutlab/reachingfurther |
| Description | RetractionWatch |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I took part in an extended interview with the popular blog RetractionWatch, which covers issues of scientific reliability and confidence in data. The blog reported at length on my 2018 paper in Current Biology, which demonstrated that a prominent piece of work in the same journal was compromised by contaminated data and therefore its findings and conclusions were unreliable. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://retractionwatch.com/2018/07/24/the-data-and-findings-are-unreliable-authors-explain-how-a-re... |
| Description | School Visit (Hammersmith) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | 30 pupils at a high school in Hammersmith attended a 40-minute lunchtime Biology Club talk delivered by the PI, with hands-on microscopical experience afterwards, and a round of questions and answers. Teachers reported students independently reading and bringing in articles from the popular scientific literature relating to the topics we covered in the meeting. Follow-up questions from students via teachers. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Sex on Earth |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | My work in connection with this award was featured as a chapter of the popular science book "Sex On Earth", by Jules Howard (Bloomsbury Sigma; 1 edition, 13 Oct. 2014). I spent several hours speaking with the author and corresponding with him about the chapter draft. I had several inquiries from members of the public about rotifers and the evolution of disease as a consequence of their exposure to the book. |
| Year(s) Of Engagement Activity | 2014,2015,2016 |
| URL | http://www.bloomsbury.com/uk/sex-on-earth-9781408193419/ |
| Description | TheScientist |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An article was published in the professional magazine 'The Scientist', detailing a paper I published in Current Biology that had implications for the practice of science in general as well as a specific scientific question. This reporting led to several follow-up requests for further information, interviews and invitations to participate in further media coverage. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.the-scientist.com/news-opinion/horizontal-gene-transfer-in-bdelloid-rotifers-questioned-... |
| Description | Work experience (BWB) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | A GCSE student from an inner London school completed a 3-week work experience placement in my lab group during the summer of 2013. He learned experimental techniques, lab safety and some basics of evolutionary biology. He also helped gather data. The student was inspired to take on STEM subjects to A-level, whereas he had previously been hesitating over his choices. |
| Year(s) Of Engagement Activity | 2013 |
| Description | imperial festival |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | I demonstrated ecological interactions between bdelloid rotifers and fungal predators as part of a display on food webs at the Imperial Festival outreach event in 2016. I spoke individually with approximately 50 members of the public, and discussed topics including natural history, biodiversity and the impact of climate change on ecology. |
| Year(s) Of Engagement Activity | 2016,2017 |
| URL | http://www.imperial.ac.uk/festival/about/festival-2017/ |
| Description | radio4 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A series of two lunchtime broadcasts on BBC Radio 4 featured research conducted as part of this project, including interviews with the PI. These were recorded when the BBC host and producer visited Imperial College London specifically to learn about this project and record a summary. Extended podcast editions of the programmes will remain available via the BBC website. We had excellent feedback from listeners via social media, demonstrating that the activity was successful at engaging the public and informing their views on evolutionary biology. The weekly listenership of Radio 4 is approximately 10 million (https://media.info/radio/stations/bbc-radio-4/listening-figures). |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.bbc.co.uk/programmes/b09sn2fn |