Computational palaeogenomics

1 PhD project offered in the IPP summer call 2019 

Scientific Background

  • Recent studies have shown significant differences in DNA methylation patterns between different ethnic groups and life-styles.

  • It is assumed that regulatory region variation correlates with relatively recent changes in the selective environment, particularly with changes in diet, environmental changes, and different life-styles.

  • DNA post-mortem damage patterns in ancient genomes can be used to computationally infer genome wide cytosine methylation maps. Palaeogenomes therefore provide the opportunity to study genetic and epigenetic variation in extinct populations and to make inference on recent selective processes in human populations.

PhD project proposal: A genome-wide view of human adaptation to novel selective environments using ancient genomes

The Palaeogentics Group of the University of Mainz is looking to recruit a PhD Students to begin in fall 2019. The PhD will be under the supervision of Prof. Joachim Burger. Whole ancient genomes will be used to understand the evolution of regulatory variation in the human genome. We will study evolutionary trajectories of adaptive regulatory region variation by analyzing time-series of prehistoric genomes extracted from archaeological skeletons.  
 
We are seeking a highly motivated person with a strong interest in human evolution, statistical genomics, computer tools, and anthropology in general. The successful candidate is expected to have a background in computational genetics, bioinformatics, statistics, or population genetics. He/she will be part of a larger research team with a strong focus on the evolution of regulatory mechanisms.

Requirements are
Master degree in biology, mathematics, informatics, statistics, or equivalent.
Skills in population genetics, biostatistics, bioinformatics.
Skills in modelling and programing are an asset.

Publications relevant to the Project

Broushaki, F., Thomas, M.G., Link, V., López, S., van Dorp, L., Kirsanow, K., Hofmanová, Z., Diekmann, Y., Cassidy, L.M., Díez-del-Molino, D., Kousathanas, A., Sell, C., Robson, H.K., Martiniano, R., Blöcher, J., Scheu, A., Kreutzer, S., Bollongino, R., Bobo, D., Davudi, H., Munoz, O., Currat, M., Abdi, K., Biglari, F., Craig, O., Bradley, D.G., Shennan, S., Veeramah, K., Mashkour, M., Wegmann, D., Hellenthal, G., Burger, J. (2016) Early Neolithic genomes from the eastern Fertile Crescent. Science 353(6298):499-503.

Hofmanová Z, Kreutzer S, Hellenthal G, Sell , Diekmann  Y, Díez-del-Molino D, van Dorp L, López S, Kousathanas A, Link V, Kirsanow K, Cassidy LM, Martiniano R, Strobel M, Scheu A, Kotsakis K, Halstead P, Triantaphyllou S, Kyparissi-Apostolika N, Urem-Kotsou DC, Ziota C, Adaktylou F, Gopalan S, Bobo DM, Winkelbach L, Blöcher J, Unterländer M, Leuenberger C, Çilingiroğlu Ç, Horejs B, Gerritsen F, Shennan S, Bradley DG, Currat M, Veeramah KR, Wegmann D, Thomas MG, Papageorgopoulou C and Burger J (2016). Early farmers from across Europe directly descended from Neolithic Aegeans. Proc Natl Acad Sci U S A 113: 6886-6891.

Wilde, S., Timpson, A., Kirsanow, K., Kaiser, E., Kayser, M., Unterländer, M., Hollfelder, N., Potekhina, I.D., Schier, W., Thomas, M.G., and Burger, J. (2014) Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. PNAS 111(13):4832 4837. 

Leonardi, M., Gerbault, P., Thomas, M. G. & Burger, J. (2012) The evolution of lactase persistence in Europe. A synthesis of archaeological and genetic evidence. International Dairy Journal 22, 88-97.

Itan, Y., Powell, A., Beaumont, M.A., Burger, J., and Thomas, M.G. (2009) The origins of lactase persistence in Europe. PLoS Computational Biology 5(8):e1000491.

Burger, J., Kirchner, M., Bramanti, B., Haak, W., and Thomas, M.G. (2007) Absence of the lactase-persistence-associated allele in early Neolithic Europeans. PNAS 104(10):3736-3741..

Contact Details

Foto: Peter Pulkowski

Prof. Joachim Burger

Email

Phone: +49 - (0)6131 – 3924489

Website: http://palaeogenetics-mainz.de