Graduate position: UOstrava.Archaeogenetics

Ph.D. student wanted: archaeogenetics and method development (admixture
> graphs)
> – application deadline: January 31, 2020
> – requirements: prior experience in analysis of genome-wide
>  archaeogenetic data; Python, R, bash
> Supervisor: Pavel Flegontov, Ph.D. (contact for
> scheduling a Skype interview)
> Duration of study: 4 years
> Institution: University of Ostrava, Ostrava, Czechia
> Collaborations: Harvard Medical School
> Net salary: 20000 CZK
> I am looking for a Ph.D. student who will start working preferably
> in March 2020. I work as a senior staff scientist in David Reich’s
> group (Harvard Medical School, Boston, USA) and as a group leader at
> the University of Ostrava, Czech Republic. The position is open at the
> University of Ostrava with a starting net pay of 20000 CZK (scholarship
> and part-time salary combined). Research stays at Harvard University
> are possible.
> Research project: While ancient DNA sequencing protocols became
> standardized and reached industrial scale, standardization of data
> analysis protocols in archaeogenetics is conspicuously lacking. Currently
> most studies are focused on the Bronze/Iron Age and historical periods
> characterized by increasing mobility and admixture of people, and the
> complexity of tasks facing a genetic data analyst ever increases. Genetic
> history of humans is best approximated as a graph including divergence
> and admixture events. Methods that test alternative graph models or search
> the model space automatically have been developed since 2012, and several
> classes of these tools exist. But a different set of analytical tools
> has become the mainstay of archaeogenetic studies: principal component
> analysis, simple statistics measuring shared genetic drift or symmetry
> of simplest population trees (e.g., f3- and f4-statistics), and qpAdm
> – a tool that tests if a target group can be fitted as a mixture of
> specified ancestral sources. A common feature of those methods is that
> they ignore the phylogeny. We show that f4-statistics are insensitive to
> large-scale admixture events under certain demographic scenarios, that
> qpAdm often lacks sensitivity for distinguishing alternative ancestral
> groups, and that some popular protocols for building admixture graphs
> (qpGraph) are flawed. We propose a method for inference of ancestral
> sources based on qpGraph and a set of strict model ranking and topology
> exploration rules. We show that this method is superior in sensitivity
> to the standard techniques and apply it for revaluating accepted views
> on the settlement of America and Bronze Age Europe. We propose an
> exhaustive simulation study of qpGraph/qpAdm, source code optimization
> for qpGraph, preparing protocol papers, and application of the novel
> tool for reanalysis of thousands of ancient genomes published.
> Recent publications (my team members are highlighted in bold):
> Flegontov P, Altınışık NE, Changmai P, Rohland N, Mallick S,
> Adamski N, Bolnick DA, Broomandkhoshbacht N, Candilio F, Culleton BJ,
> Flegontova O, Friesen TM, Jeong C, Harper TK, Keating D, Kennett DJ,
> Kim AM, Lamnidis TC, Lawson AM, Olalde I, Oppenheimer J, Potter BA,
> Raff J, Sattler RA, Skoglund P, Stewardson K, Vajda EJ, Vasilyev S,
> Veselovskaya E, Hayes MG, O’Rourke DH, Krause J, Pinhasi R, Reich D§,
> Schiffels S§. (2019) Paleo-Eskimo genetic ancestry and the peopling of
> Chukotka and North America.  Nature, 570:236-240.
> Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M,
> Pryce TO, Willis A, Matsumura H, Buckley H, Domett K, Nguyen GH, Trinh HH,
> Kyaw AA, Win TT, Pradier B, Broomandkhoshbacht N, Candilio F, Changmai P,
> Fernandes D, Ferry M, Gamarra B, Harney E, Kampuansai J, Kutanan W, Michel
> M, Novak M, Oppenheimer J, Sirak K, Stewardson K, Zhang Z, Flegontov P,
> Pinhasi R, Reich D. (2018) Ancient genomes document multiple waves of
> migration in Southeast Asian prehistory.  Science, 361:92-95.
> Pavel Flegontov, PhD
> Senior staff scientist, David Reich Lab
> Department of Genetics, Harvard Medical School,
> Boston, MA, USA
> Group leader,
> Department of Biology and Ecology,
> University of Ostrava,
> Ostrava, Czech Republic
> Pavel Flegontov <>