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Oliver Smith

Hi there, and welcome to my eportfolio.

After obtaining a BA in Egyptian archaeology from the University of Liverpool and a MSc in Biomedical Egyptology from the University of Manchester, I obtained my my PhD in April2013, in plant archaeogenetics at the University of Warwick School of Life Sciences. I am currently a postdoctoral researcher with the Allaby Research Group, primarily researching plant evolution / adaptation through archaeogenetic (ancient DNA / RNA) analysis. My research so far focuses on genome reconstruction, small RNA activity, and the identification of epigenetically-mediated stress responses in ancient Egyptian barley (Hordeum vulgare), hence my thesis (see below).

As a collaboration between the Allaby and Pallen Research Groups, I am also investigating archaeological metagenomics from North Sea sediment cores and human pathogens from archaeological remains. Over the coming years I will be continuing this research, and investigating plant adaptation in ancient Egyptian sorghum.

Archaeoepigenetics: Detection of Epigenetics in Archaeogenetic Systems

Archaeogenetic analysis typically focuses on ancient DNA to identify phylogeny, population movements, evolution and adaptation. Recent archaeogenetic studies show that massively parrallel ('high-throughput') sequencing technologies, usually used for deep analysis of intact genomes, are equally applicable to the study of ancient genetic material. Genomic study in general has recently come to realise the potential significance of gene interaction and regulation and how some mechanisms, for example epigenetic regulation, might actually be forefront 'drivers' of the evolutionary process.

My research focuses on the presence and function of small (~18-24 nt), regulatory RNAs - specifically microRNAs (miRNA) and short interfering RNAs (siRNA), in a potentially drought-stressed cultivar of ancient Egyptian barley. Grain samples from Qasr Ibrim, a frontier fort on what was the Egyptian / Nubian border show an unusual developmental irregularity which could be an epigenetically-mediated stress response to the extremely arid environment. Ironically, this aridity has contributed to the unusually high level of nucleic acid preservation in our samples which allows us to examine DNA and RNA in detail (RNA is usually much more unstable than DNA). In another twist to this tale, the site is now mostly underwater (after the creation of Lake Nasser in the 1960s).

This study of the 'archaeoepigenome' is the first of its kind. Until recently, study of even degraded, let alone ancient RNA (as opposed to DNA) was considered irrelevant in terms of a) limited preservation of ancient RNA and b) useful information to be gleaned from it. Recent work has shown that in certain tissues such as seed endosperm, RNA survives with comparable quantity and integrity to that of DNA. My results point towards interesting microRNA interactions unique to our ancient sample along certain developmental pathways, and concurrent validation of siRNA profiles along certain non-coding regions (awaiting the results of genomic methylation patterns). The dataset has also allowed me to almost completely (~97%) reconstruct an ancient viral genome embedded within the grain, and investigate plant-mediated viral defense through RNA interference (RNAi).

Researcher Details

PhD awarded: April 2013

Thesis title: Small RNA-Mediated Regulation, Adaptation and Stress Response in the Barley Archaeogenome

Supervisor: Dr. Robin G. Allaby

Department: School of Life Sciences (formerly Warwick HRI)

Funding body: BBSRC (Doctoral Training Grant)

Publications (link)

Oliver Smith

o dot smith dot 1 at warwick dot ac dot uk