New data modalities in meiofaunal phylogenomics

Project Background 

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 2/3 of all animal phyla (of which 7 are exclusively meiofaunal), and with on the order of 105-106 species represented, most still undescribed. Their extraordinary diversity and the comparative lack of research attention makes them a largely untapped well of evolutionary and ecological insights. 

In particular, many animal meiofauna still take unresolved positions in the animal tree of life, even after decades of molecular phylogenetic research. This is not only because of difficulties in obtaining and identifying material suitable for genomics, but also because of intrinsic properties of their genomes. In molecular phylogenies, most meiofaunal lineages (perhaps as a consequence of short generation times) demonstrate extraordinarily fast rates of substitution, and in some cases, show biased amino acid composition, often causing tree-inference to be misled.  

Sequencing and sample preparation technology has now progressed to the point that it is possible to generate a highly contiguous, even chromosomal, representation of meiofaunal species’ genomes, starting from a single individual. In addition, recent advances in phylogenomics have shown that many refractory problems are beginning to find solutions from genome data beyond coding-gene multiple sequence alignments. In particular, gene family births, duplications, and losses, and shared changes in synteny (the linear arrangement of genes along chromosomes) are showing themselves as rich sources of phylogenetic signal, which have the potential to be resilient to the traditional bugbears of phylogenomics. 

Project Aims and Methods 

A core question of interest in this PhD is how well phylogenies built from newer genome-wide data modalities such as shared synteny changes and gene content recapitulate results from conventional sequence-alignment based phylogenies. Defining the temporal pace of genomic rearrangements and genic innovation through geological time – e.g. whether generally “clocklike” and/or correlated to sequence substitution, versus more prone to episodic bursts, high cross-taxon variation, and convergence – is another open question of core importance, which may in principle be interrogated rigorously with use of time-calibrated phylogenies. Such studies will be useful in critically interpreting the large number of studies using non sequence-alignment based inferences which can be anticipated in the genomic age. 

Students interested in shaping this project to suit their existing research interests/expertise are welcome, and are encouraged to contact both supervisors to discuss their original ideas. In particular, given the diversity of meiofauna, it is possible to select from among many diverse taxonomic groups or phylogenetic problems of focal interest – although practical constraints such as average genome size and availability of material should be considered. Focussing on clades spanning a combination of macro- and meiofaunal members is also a viable direction. 

Candidate requirements 

Prior experience with molecular phylogenetics, molecular biology protocols, bioinformatics, and microscopy or fieldwork will all be beneficial to this project. We especially welcome applications from students with basic proficiency with the UNIX command line and at least one programming language such as Python, R, or Rust. However, enthusiasm, critical thinking, and intellectual curiosity for the subject are ultimately more important than any specific prior technical skill. 

Project partners  

Over 150 PhD students are linked with the Natural History Museum for their doctoral research, including students from 8 Doctoral Training Programmes. We have a welcoming and active student community, 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.   

Training 

In this project, you will gain a blend of classical and cutting-edge technical expertise, learning how to sample and observe marine meiofauna in field settings (both domestic and international), identify them morphologically, and preserve and process them for whole-genome assembly, annotation, and chromosomal scaffolding using Hi-C. You will computationally compare 10s of species’ genomes, organizing and scrutinising orthology assignments, launching whole-genome multiple alignments, and testing various approaches for inferring macro- and micro-synteny events. Overall, the skills you will gain (including programming skills), are highly transferrable and sought after, enabling a diversity of possible careers, ranging from academic research, to data scientist or molecular biologist in the biotechnology sector.

How to apply

Apply for this project here.

The application deadline is Tuesday 9 January 2024 at 23.59 GMT.

Interviews will take place from 26 February to 8 March 2024. For more information about the NERC GW4+ Doctoral Training Partnership please visit https://www.nercgw4plus.ac.uk.

If you are interested in applying, you must complete the Personal Statement form.

Please also complete the applicant's questionnaire GW4+ DTP PhD applicants questionnaire - 2023-24.

For more information on who can apply please visit the GW4+ page: Apply - NERC GW4+.

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