Tom Gilbert

Tom Gilbert is an Honarary Fellow: Department of Biology, University of York - see BioArCh.

I obtained my BA in Biological Sciences from Oriel College, University of Oxford, predominantly focusing on the epidemiology of infectious disease, and the behavioural ecology of amphibious fish. Following this I moved over to more molecular biology based research, undertaking a D.Phil at Oxford’s Zoology Department under the supervision of Alan Cooper. My thesis, entitled ‘An assessment of the use of human samples in ancient DNA research’ focused on the characterization of some of the biochemical and contamination related problems of ancient human DNA research.

In 2003 I moved to the University of Arizona, to undertake a post-doctoral position under Dr Mike Worobey. In this time I predominantly focused my research on teasing nucleic acids (both DNA and RNA) out of archival formalin fixed human tissues, including a huge collection from the former Belgian Congo. The reason for doing this – the recovery and analysis of historic viral sequences, particularly HIV-1 – has been fairly productive and remains one of my key research interests.

In 2005 I commenced a Marie Curie Intra-European Fellowship at the Department of Biology, University of Copenhagen, and in late 2007 was awarded one of 3 ‘Skou’ Associate Professor Awards by the Danish National Science Foundation. This has enabled me to run a research group with a variety of biological, anthropological and archaeological interests.

Interests

The underlying theme of my research interests is the investigation of ecological, evolutionary biological, anthropological and archaeological questions through the exploitation of tissues and other materials that are conventional deemed unsuitable for nucleic acid-based analyses. In particular, I aim to both investigate long-standing questions, and open up new research frontiers through the development of new, optimization of extant, and coupling of previously disparate techniques. I believe that the most efficient means to obtain my research goals, is through collaboration with, and information transfer between some of the leading researchers their respective disciplines. Therefore in light of my aims and interests, I have built up a network of geographically widespread, close collaborators, both within the UK, in Europe, and in the Americas and Australia.

Current Research projects

Developmental related

The potential and limitations of sub-optimal materials for use in genetic analyses. Including bone, keratinous tissues, chitinous materials, leather, wool.
The customization of the Roche FLX, Illumina Solexa and Applied Biosystems SOLiD sequencing platforms to ancient, forensic and other degraded DNA studies. Examples include customizing the FLX to simultaneously co-sequence thousands of independent, homologous PCR products, using the FLX to rapidly generate complete ancient mtDNA genomes, and using the FLX to rapidly generate complete ancestral viral genomes from formalin fixed materials.
The postmortem degradation, repair, and subsequent retrieval of nucleic acids

Biology

Phylogenetic placement and population genetic analyses of extinct mammalian megafauna using complete mtDNA analysis. Taxa under study include killer whales, narwhale, reindeer, woolly and extant rhinoceroses, saiga antelope, and musk oxen and their related genera. The research is principally based on DNA recovered from ancient bone and hair material.
Phylogenetic and population genetic analyses of the giant and collosal squid species- This research exploits the use of DNA recovered from archival beak fragments as a means to greatly expand the dataset available for research.
Studying the evolutionary history of viruses using DNA sequences recovered from archival (principally early 20th century formalin fixed) specimens. Specific interest in HIV-1 using preserved materials obtained from former Zaire.

Archaeology and Anthropology

Documenting the genetic background and time of arrival of the first humans in the Americas and Greenland, using DNA recovered from trace biological materials, including hair and coprolites.
The domestication of maize, grapes and any other plants I can get a decent number of well preserved seeds from

References

Gilbert MTP et al. (2008) Paleo-Eskimo MtDNA genome reveals matrilineal discontinuity in Greenland. Science 320:1787-1789
Gilbert MTP et al. (2008). Intraspecific Phylogenetic Analysis of Siberian Woolly Mammoths Using Complete Mitochondrial Genomes. Proc Natl Acad Sci USA 105:8327-8332 Gilbert MTP et al. Science 329:786-789
Buckley M et al. (2008) Comment on “Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry”. Science 319:33c
Melchior L (2008) Rare mtDNA haplogropus and genetic differences in rich and poor danish Iron-age villages.
Am J Phys Anthropol 135:206-215 Malmström H et al. (2008) Barking up the wrong tree: Modern northern European dogs fail to explain their origin. BMC Evol Biology 8:71
Gilbert MTP et al. (2007) Whole-Genome shotgun sequencing of mitochondria from ancient hair shafts. Science 317:1927-1930
Gilbert MTP et al. (2007) Emergence of HIV/AIDS in the Americas and Beyond. Proc Natl Acad Sci USA 104:18566-18570
Wilson AS et al. (2007) Inca child sacrifice: isotopic and DNA evidence for ritual sequences. Proc Natl Acad Sci USA 104:16456-16461
Johnson SS et al. (2007) Ancient Bacteria show evidence of DNA repair. Proc Natl Acad Sci USA 104:14401-14405
Gilbert MTP et al. (2007) The isolation of nucleic acids from fixed, paraffin embedded tissues – which methods are useful when? PLoS ONE 6:e537
Willerslev E et al. (2007) Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland Science 317:111-114
Malmström H et al. (2007) More on contamination: Asymmetric molecular behaviour as a mean to identify authentic ancient human DNA. Mol Biol Evol 24:998-1004
Gilbert MTP et al. (2007) mtDNA from hair and nail clarifies the genetic relationship of the 15C Qilakitsoq Inuit mummies. Am J Phys Anthropol 133:847-853
Binladen J et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2:e197
Gilbert MTP et al. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res 35:1-10
Vuissoz A et al. (2007) The survival of PCR-amplifiable DNA in cow leather. J Archeol Sci 34:823-829
Shapiro B et al. (2006) No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al). Int J Inf Dis 10:334-335
Gilbert MTP et al. (2005) Assessing ancient DNA studies. Trends Ecol Evol 20:541-544 Machado CA et al. (2005) The coevolutionary history of the fig-fig wasp mutualism: new insights from Neotropical species. Proc Natl Acad Sci USA 102:6558-6565
Gilbert MTP et al. (2005) Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy. J Archaeol Sci 32:783-795
Gilbert MTP et al. (2005) The long-term survival of ancient DNA in Egypt: Response to Zink and Nerlich 2003. Am J Phys Anth 128:100-114 Shapiro B et al. Science 306:1561-1565