About the Project
We are seeking a highly motivated PhD student for a research project in the population genomics of Native Americans from South America.
Supervisors:
Dr. Shigeki Nakagome, School of Medicine, Trinity College Dublin
(Please see the details of research: https://sites.google.com/site/shigekinakagome/)
Professor Daniel Bradley, School of Genetics and Microbiology, Trinity College Dublin
(Please see the details of research: http://www.gen.tcd.ie/molpopgen/dan.php)
Project Summary:
The peopling of South America is of interest in understanding migration history from Eurasia to the Americas and adaptation to new environments including climate, diets, and pathogens. This PhD project will generate whole-genome sequence data from 32 populations and 500 individuals living in South America. This will give one of the largest whole-genome data sets in Native Americans and provide an opportunity to compare genomic variation between people from Eurasia and the Americas and reconstruct the evolutionary history of that continent. The research will leverage statistical and population genetic analyses, integrating them into systematic ways to 1) model the demographic history of Native Americans, 2) detect signatures of natural selection unique to Native Americans, and 3) infer the mode and tempo of natural selection on beneficial mutations. This PhD project will have a potential extension to whole-genome sequencing of ancient Native Americans from the 18th century before strong admixture with western Eurasians occurred.
We invite applicants from highly motivated and outstanding students with a strong background and interest in population genetics, bioinformatics, and statistics. Students from related areas including physics or mathematics are also welcome to apply.
Applicants should send a CV, a statement of their research interests, and a cover letter to Shigeki Nakagome ([Email Address Removed]). Candidate selection will begin immediately, but applications will be considered until the position is filled.
References
• Kernel approximate Bayesian computation in population genetic inferences.
Nakagome S., Fukumizu K., Mano S. (2013) Statistical Applications in Genetics and Molecular Biology, 12(6):667-678.
• Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.
Nakagome S., Sato T., Ishida H., Hanihara T., Yamaguchi T., Kimura R., Mano S., Oota H., The Asian DNA Repository Consortium. (2015) Molecular Biology and Evolution, 32(6):1533-1543.
• Deep history of East Asian populations revealed through genetic analysis of the Ainu.
Jeong C., Nakagome S., Di Rienzo A. (2016) Genetics, 202(1):261-272.
• Estimating the ages of selection signals from different epochs in human history.
Nakagome S., Alkorta-Aranburu G., Amato R., Howie B., Peter B.M., Hudson R.R., Di Rienzo A. (2016) Molecular Biology and Evolution, 33(3):657-669.
• A time transect of exomes from a Native American population before and after European contact.
Lindo J., Huerta-Sánchez E., Nakagome S., Rasmussen M., Petzelt B., Mitchell J., Cybulski J., Willerslev E., DeGiorgio M., Malhi R. (2016) Nature Communications, 7:13175.
• Upper Palaeolithic genomes reveal deep roots of modern Eurasians.
Jones E.R., Gonzalez-Fortes G., Connell S., Siska V., Eriksson A., Martiniano R., McLaughlin R.L., Gallego Llorente M., Cassidy L.M., Gamba C., Meshveliani T., Bar-Yosef O., Müller W., Belfer-Cohen A., Matskevich Z., Jakeli N., Higham T.F., Currat M., Lordkipanidze D., Hofreiter M., Manica A., Pinhasi R., Bradley D.G. (2015) Nature Communications, 6:8912.
• Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome.
Cassidy L.M., Martiniano R., Murphy E.M., Teasdale M.D., Mallory J., Hartwell B., Bradley D.G. (2015) Proceedings of the National Academy of Sciences of the United States of America, 113(2):368-373.
• Genomic signals of migration and continuity in Britain before the Anglo-Saxons.
Martiniano R., Caffell A., Holst M., Hunter-Mann K., Montgomery J., Müldner G., McLaughlin R.L., Teasdale M.D., van Rheenen W., Veldink J.H., van den Berg L.H., Hardiman O., Carroll M., Roskams S., Oxley J., Morgan C., Thomas M.G., Barnes I., McDonnell C., Collins M.J., Bradley D.G. (2016) Nature Communications, 7:10326.
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