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Plastic genomes: how do animals respond to their environment?

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  • Full or part time
    Dr E.J.. Duncan
    Dr A.D. Peel
  • Application Deadline
    No more applications being accepted
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

All animals respond to their environment, but some are able to radically change their biology, behaviour, reproduction and even the way they develop in response to environmental change. This responsiveness is called phenotypic plasticity.

Phenotypic plasticity is important in human health, animal development and agriculture and may crucial to understanding how animals respond rapidly to new and changing environments; a fundamental question in ecology, conservation biology, and evolution. Despite the importance of phenotypic plasticity we know very little about how plasticity works, how plasticity is encoded in the genome and how it evolved. In my lab we aim to address these questions using insect models, such as the honeybee and pea aphid [e.g. 1, 2-5].

The pea aphid (Acyrthosiphon pisum) is a remarkable animal, it usually reproduces asexually (viviparously), but in response to environmental change (decreasing temperatures and short day lengths) the pea aphid is able to reproduce sexually (oviparously); producing eggs. This remarkable and unusual reproductive strategy allows for rapid production of a large number of offspring, allowing aphids to rapidly colonise a host plant. Because of this plasticity aphids, including the pea aphid, are significant crop pests that cause hundreds of millions of pounds of crop damage per year.

Embryos produced sexually or asexually develop in completely different environments; embryos produced asexually develop inside their mother, protected from the environment. Nutrients are supplied directly to the embryo and development is rapid (10-15 days). In contrast embryos that develop as a result of sexual reproduction (sexual morphs) develop externally within a large yolky egg and diapause over winter such that development takes 75-100 days. The way these early embryos undergo early development is also strikingly different between sexual and asexual morphs, and we see substantial differences in expression of genes controlling early development between sexual and asexual morphs [3, 6]. Our data, and that of others, suggests that the phenotypic plasticity and the evolution of asexual reproduction in the pea aphid have resulted in extensive rewiring of early developmental pathways. This is the first time that two distinct ways of controlling development have been found in a single animal, and encoded in a single genome. The pea aphid is, therefore, an utterly unique system to understand not only how plasticity works, but also how plasticity has affected the evolution of key developmental pathways.

There is a lot of scope within this area of research and the exact project and experimental approach will be developed in collaboration with the successful student. Broadly, you will use a combination of techniques (e.g. transcriptomics and in situ hybridization to measure gene expression, comparative genomics to understand the evolutionary history of genes, live embryo imaging to track early development as well as RNA interference and CRISPR/Cas9 mediated genome editing to assess gene function) to determine more about how plasticity works in this species and, perhaps more importantly, how these two different early developmental pathways evolved and how they are encoded in a single genome.

Keywords: evo-devo, axis formation, embryo patterning, pea aphid, insect, genomics, transcriptomics, phenotypic plasticity, epigenetics.

Funding Notes

Project is eligible for funding under the FBS Faculty Studentships scheme. Successful candidates will receive a PhD studentship for 4 years, covering fees at UK/EU level and stipend at research council level (£14,777 for 2018-19).

Candidates should have, or be expecting, a 2.1 or above at undergraduate level in a relevant field. If English is not your first language, you will also be required to meet our language entry requirements. The PhD is to start in Oct 2018.

Please apply online here https://studentservices.leeds.ac.uk/pls/banprod/bwskalog_uol.P_DispLoginNon Include project title and supervisor name, and upload a CV and transcripts.


1) Duncan, et al., (2016), Nat Commun. 7: p. 12427.
2) Duncan, et al., (2014), J Exp Zool B Mol Dev Evol. 322(4): p. 208-20.
3) Duncan, et al., (2013), Dev Biol. 377(1): p. 245-61.
4) Cameron, et al., (2013), Apidologie. 44(4): p. 357-366.
5) Cameron, et al., (2013), BMC Genomics. 14: p. 903.

How good is research at University of Leeds in Biological Sciences?

FTE Category A staff submitted: 60.90

Research output data provided by the Research Excellence Framework (REF)

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