James A. Fellows Yates, B.Sc., M.Sc.

Department of Archaeogenetics

Main Focus

My current area of research is centered on the ancient DNA content of fossilised dental plaque, also known as dental calculus. This work is a part of the DAG's "Evolution and Ecology of the Human Oral Microbiome" project, which contains samples spanning from the Palaeolithic to Modern day. I am primarily exploring how we can analyse and authenticate the complex genetic makeup of this material through shotgun metagenomics.

I am also a co-developer of nf-core/eager, a fully reproducible and and portable pipeline for doing standard processing of aDNA data. I have also created an interactive tool for viewing the output of the ancient metagenomics pipeline HOPS, called MEx-IPA

Previously, I have worked on Late Pleistocene woolly mammoth mitochondrial genomes, as well as testing collagen ‘fingerprinting’ methods (ZooMS) on burnt skeletal remains.

My general interests are:

Biomolecular archaeology (Ancient DNA, Palaeoproteomics, Stable Isotopes)
Prehistory
Oral Microbiomes
Bacterial genomics
Metagenomics

Curriculum Vitae

My CV can be downloaded here

Publications

Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8(1), 31. https://doi.org/10.1038/s41597-021-00816-y

Swift, J.A; Bunce, M.; Dortch, J.; Douglass, K.; Faith, J.T.; Fellows Yates, J.A; Field, J.; Haberle, S.G; Jacob, E.; Johnson, C. N; Lindsey, E.; Lorenzen, E.D.; Louys, J.; Miller, G.; Mychajliw, A.M.; Slon, V.; Villavicencio, N.A.; Waters, M.R.; Welker, F.; Wood, R.; Petraglia, M.; Boivin, N.; Roberts, P. (2019). Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene. Bioscience. https://doi.org/10.1093/biosci/biz105

Mann, A. E., Sabin, S., Ziesemer, K., Vågene, Å. J., Schroeder, H., Ozga, A. T., Sankaranarayanan, K., Hofman, C. A.; Fellows Yates, J. A ,… Warinner, C. (2018). Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports, 8(1), 9822. https://doi.org/10.1038/s41598-018-28091-9

Warinner, C., Herbig, A., Mann, A., Fellows Yates, J. A., Weiß, C. L., Burbano, H. A., … Krause, J. (2017). A Robust Framework for Microbial Archaeology. Annual Review of Genomics and Human Genetics, 18, 321–356. https://doi.org/10.1146/annurev-genom-091416-035526

Fellows Yates, J. A., Drucker, D. G., Reiter, E., Heumos, S., Welker, F., Münzel, S. C., … Krause, J. (2017). Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes. Scientific Reports, 7(1), 17714. https://doi.org/10.1038/s41598-017-17723-1

Conferences and Workshops

Fellows Yates. J.A. et al. "Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA" Conference presentation, International Symposium for Biomolecular Archaeology (ISBA8), September 2018, Jena, Germany

Fellows Yates, J.A. et al. "Palaeogenomic Investigation Of 50,000 Years Of The Human Oral Microbiome In The Iberian Mediterranean" Conference presentation, Annual Meeting of the European Association for Archaeologists (EAA 2018), September 2018, Barcelona, Spain

Fellows Yates. J.A.; et al. "Reconstruction of Oral Microbiomes from Extinct and Extant Anthropoids through ancient DNA" Conference poster Society for Molecular Biology and Evolution (SMBE18), July 2018, Yokohama, Japan

Fellows Yates et al. (2017) "Central European Late Pleistocene Woolly Mammoths: Insights from ZooMS, Stable Isotope and aDNA data" Workshop presentation, Megafauna and Methods Workshop, Max Planck Institute for the Science of Human History, Jena, Germany

Fellows Yates et al. (2016) "Full Mitochondrial Genomes of Central European Upper Palaeolithic Woolly Mammoths (Mammuthus primigenius)" Conference Poster, International Symposium for Biomolecular Archaeology (ISBA7), University of Oxford, Oxford, United Kingdom doi:dx.doi.org/10.13140/RG.2.2.33453.28648

Education

2015 - Current Ph.D. Archaeogenetics, MPI for the Science of Human History, Jena

Thesis (Provisional): Evolution of the Oral Microbiome

2013-2015 M.Sc. Naturwissenschaftliches Archäologie / Archaeological Sciences, Universität Tübingen (DE)

Thesis: Full Mitochondrial Genomes of Upper Palaeolithic Central EUropean Woolly Mammoths (Mammuthus primigenius)

2010-2013 B.Sc. Bioarchaeology, University of York (UK)

Thesis: “It Will Not Be Possible To Use Zooarchaeology By Mass Spectrometry (ZooMS) To Identify Species In Samples Of Cremated Bone That Have Been Burnt Higher Than 155^oC”

Additional

2014-2015 Stable Isotopes Student Research Assistant - Universität Tübingen

AG Biogeologie - sample preparation, collagen extraction, data curation