Transforming meiofaunal molecular systematics and community ecology through nanopore-based transcriptome skimming

Project description

Aquatic microinvertebrates living in sediments and soils, sometimes known as meiofauna, represent one of Earth’s largest and least-known reservoirs of animal biodiversity, with over two-thirds of all animal phyla and on the order of 10⁵-10⁶ species represented, most still undescribed.

With such high diversity and dwindling taxonomic expertise, technological innovations will be required to unlock the large potential insights these communities can yield in evolutionary and ecological research.

Low-depth long-read transcriptome sequencing, with only 10,000s of reads per sample, is sufficient to assemble hundreds of highly expressed genes, including all or nearly all mitochondrial protein-coding genes, nuclear rRNAs, and many other phylogenetically useful housekeeping genes, without any targeted PCR. This allows any specimen to be phylogenetically placed with high confidence, even in taxa where 'universal' primers fail and can recover sequences of symbionts and gut contents simultaneously.

Combined with the high accuracy, throughput, and accessibility of nanopore sequencing, protocols that enable large numbers of specimens to be transcriptome-skimmed, exploiting liquid handling robots, and combinatorial barcoding approaches borrowed from single-cell RNA-seq, may be transformative for the study of meiofaunal biodiversity.

The successful candidate will participate in developing this technique, already validated with pilot data, designing, overseeing and implementing transcriptome skimming experiments at the Museum’s molecular laboratories. At Queen Mary University of London (QMUL), you will develop bespoke bioinformatics tools to quality-control, assemble, and mine these data for phylogenetic markers and to iteratively build very large (100,000+ specimen) phylogenies. There is considerable potential for students to develop taxonomic expertise in parallel and to participate in leading domestic and international fieldwork, focusing on temperate rainforests and marine seagrass meadows, two globally threatened habitats of outsized ecological importance.

Research environment

Over 150 PhD students are linked with the Museum for their doctoral research, including students from eight Doctoral Training Programmes. We have a welcoming and active student community, a dedicated Graduate Centre for working and socialising and an annual calendar of student activities and workshops. Students are also encouraged to participate in wider Museum activities, including Museum Lates, Dinosnores and the Graduate Centre Explorers pilot programme.

The School of Biological and Behavioural Sciences at Queen Mary is one of the UK’s elite research centres, according to the 2021 Research Excellence Framework (REF). They offer a multi-disciplinary research environment and have approximately 150 PhD students working on projects in the biological and psychological sciences. Students have access to a variety of research facilities supported by experienced staff, as well as a range of student support services. Your work will benefit from access to modern genomics labs and the 13,000-core Apocrita HPC cluster.

You will join a dynamic and supportive team of collaborative researchers who enjoy life and doing impactful, innovative science.  You will be co-supervised in the research groups of Dr Christopher Laumer, a new research fellow at the Museum, leading research in meiofaunal biodiversity, systematics, and comparative genomics, with strong side interests in molecular wet-lab method development and Dr Yannick Wurm, who leads a research group at QMUL in evolutionary genomics, bioinformatics, and social insect biology

Training and development

PhD students will become part of Queen Mary’s Doctoral College, which provides training and development opportunities, advice on funding, and financial support for research. Students also have access to a Researcher Development Programme designed to help recognise and develop key skills and attributes needed to effectively manage research and plan for the next stages of their careers.

You will obtain a broad range of interdisciplinary and transferable training. You will develop and implement new approaches, receive training in molecular biology, genomics, bioinformatics, data science, software development, scientific communication and related disciplines. You will collaborate for some aspects of the project, and develop the critical skills needed to lead other aspects. You will have the opportunity to develop your communication skills by drafting and writing manuscripts and reports, and present your work during regular laboratory-level meetings and UK and international conferences. You will also have the opportunity to help as a teaching assistant.

With co-supervision between two research groups with expertise in wet-lab and bioinformatic method development research, this PhD will offer the successful candidate an excellent opportunity to develop an interdisciplinary skill set well-suited to biodiversity genomics using state-of the art methodologies. Furthermore, there is an opportunity to acquire complementary microscopy, fieldwork, and museum specimen-based skill sets under the supervision of Dr Christopher Laumer.

Funding

The studentship is funded by the Royal Society through a University Research Fellowship. It will cover Home tuition fees and an annual tax-free maintenance allowance for four years at the UKRI rate with a London allowance (£20,662 in 2023/2024). International tuition fees are unfortunately not covered.

Eligibility and applying

Applications are invited from outstanding candidates interested in interdisciplinary life sciences research, with or expecting to receive a first or upper-second class honours degree in an area relevant to the project, including organismic and evolutionary biology, ecology, molecular biology, software development, computational biology, or bioinformatics. Motivation and the ability to think rigorously are more important than specific technical expertise or experience.

A masters degree or similar experience is desirable but not essential. Past research experience (internships or summer studentships) involving molecular lab work and/or basic bioinformatics will be valuable.

Applicants from outside of the UK are required to provide evidence of their English language ability. Please see QMUL's English language requirements page for details.

Informal enquiries about the project are very welcome and can be sent to Dr Christopher Laumer or Professor Yannick Wurm. Applicants are encouraged to explain their motivations for applying to this specific project and to discuss their own original ideas for the project. Formal applications must be submitted through our online form by the stated deadline, including a CV, personal statement and qualifications.

The School of Biological and Behavioural Sciences is committed to promoting diversity in science; we have been awarded an Athena Swan Silver Award. We positively welcome applications from underrepresented groups.