The structure of the Holobiont Tree-of-Life


   Department of Life Sciences

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  Dr A Vogler, Dr Matthew Ryan, Prof James Rosindell  No more applications being accepted  Funded PhD Project (UK Students Only)

About the Project

What is the structure of the Tree-of-Life and how do its components interact? Holobionts are composed of distantly related organisms joined in various mutualistic or antagonistic relationships that were independent of each other for most of their evolutionary history. However, when joined in the holobiont their independently evolved traits are interacting to various degree of closeness, and this is when co-evolutionary processes set in. Only the revolution of taxonomic DNA sequencing of recent years has allowed to estimate the Tree-of-Life to any degree of completeness for the macro- and microbiological holobiont lineages together. This provides the framework for studying the legacy of phylogenetic history on the interacting partners and their traits, which will ultimately reveal the extent to which holobionts are composed of independently evolved and coevolved components. 

The focus of this study is on the most diverse lineages of interacting organisms that make up key ecosystem processes: insects, fungi, and bacteria. Ongoing research in each of these lineages is at the cusp of major insights into their phylogeny, and this project will draw on available resources and ongoing research to obtain detailed trees for each lineage. In a first step, the student will scan the literature for bacterial and fungal lineages known to be functionally connected with insects, using sources from detailed ecological and coevolutionary studies of symbiotic systems. Next, these searches will be extended to the co-distributed components gathered from two sources: (a) metabarcoding of insect specimens using fungal and bacterial specific primers, and (b) whole genome and metagenomic sequencing of insects that also produce sequences of microbial origin associated with the target organism. The latter will draw on the work of the Darwin Tree-of-Life (DTOL) project that is projected to produce several thousand genome sequences of insects but largely discards data of presumed microbial origin. The collections at NHM and CABI will be the source for metabarcoding approaches of a wider range of species.

The information is compiled in large bi- and tri-partite networks, for a broad-scale perspective of insect-fungal-bacterial interactions at the level of deep lineages: which groups co-occur and what are their traits? The patterns of co-distribution will be assessed for alternative correlations with either phylogeny or ecology, by scoring ecological functions such as pollination (mutualistic), plant pathogens (antagonistic), or organic matter decomposition (neutral) etc., and habitats such as vegetation, the soil or freshwater. Based on this information, we will ask if the composition of the holobiont can be predicted in broad terms from the Tree-of-Life and what are the driving forces and evolutionary constraints of holobiont composition. This lays the foundation for more detailed studies at the species level (in part already ongoing within the Centre), to search for the co-evolved traits, ultimately at the genomic and metabolomic levels.

The student would join the Leverhulme Centre for the Holobiont (www.imperial.ac.uk/holobiont/), a multi-institutional research centre devoted to understanding interactions between multicellular hosts and their microbial symbionts.

Informal enquiries are welcomed and should be sent to Prof Alfried Vogler ([Email Address Removed])

How to apply:

Please email Prof Alfried Vogler ([Email Address Removed]) and include in your application:

  • Statement of Purpose
  • Your CV
  • At least two references to be sent directly to Alfreid Vogler from the referees.

Full applications made before 15th January will be considered at any time.

Funding and eligibility:

A fully funded 4 years Leverhulme Studentship, including tuition fees and a standard research council stipend. The fees and stipend cover UK home applicants and standard research council eligibility criteria apply:

https://www.ukri.org/what-we-offer/developing-people-and-skills/find-studentships-and-doctoral-training/get-a-studentship-to-fund-your-doctorate/

The successful applicant must hold, or be expected to complete, an MSc/Mres with merit/distinction in a relevant subject area of evolutionary biology and systematics. 


Biological Sciences (4)

References

Ceballos-Escalera, A. J. Richards, M.B. Arias, D.J.G. Inward, and A.P. Vogler. 2022. Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88, 1
Arribas, P., ... and A. P. Vogler. 2020. Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari. Mol. Biol. Evol., 37, 683-694
Vancaester, E., Blaxter, M. 2023. Wolbachia are common bacterial endosymbionts that manipulate reproductive biology in their hosts. PLOS Biology 21(1) e3001972
Challis R, Kumar S, Sotero-Caio C, Brown M, Blaxter M. Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Wellcome Open Res. 2023 Jan 17;8:24. doi: 10.12688/wellcomeopenres.18658.
Peck, L.D., Nowell, R.W., Flood, J., Ryan M.J. & Barraclough, T. Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides. BMC Genomics 22, 404 (2021). https://doi.org/10.1186/s12864-021-07700-4

Rowena Hill, Quentin Levicky, Frances Pitsillides, Amy Junnonen, Elena Arrigoni, J Miguel Bonnin, Anthony Kermode, Sahr Mian, Ilia J Leitch, Alan G Buddie, Richard J A Buggs, Ester Gaya. Tapping culture collections for fungal endophytes: First genome assemblies for three genera and five species in the Ascomycota. Genome Biology and Evolution, Volume 15, Issue 3, March 2023, evad038, https://doi.org/10.1093/gbe/evad038
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 About the Project