The proposed research is intended to develop mathematical and statistical methods for analyzing DNA sequence data from individuals sampled from several closely related populations. One part of the proposed research will be to develop methods that allow inference of past and present patterns of migration and admixture. The methods will be applied to DNA sequences from individuals from several human populations and from extinct human relatives, including Neanderthals and Denisovans (a distant relative of Neanderthals). The proposed research is intended to provide improved ways of understanding the history of humans and their close relatives. One goal will be to characterize the admixture that occurred between humans, Neanderthals, Denisovans, and other extinct human relatives. A second goal will be to identify genes in the human genome that recently increased in frequency under the effect of natural selection since the separation from Neanderthals and Denisovans but before the divergence of modern human populations. Although these methods are motivated by the recently available genomes from Neanderthals and Denisovans, they will be applicable to other groups of closely related species as more genomic data becomes available. The second part of the proposed research will be to develop methods for using DNA sequence data from a single species to detect evidence of a recent expansion in geographic range either into an empty habitat or a habitat already containing a resident admixing species. The goal will be to determine whether a range expansion has taken place, where its geographic origin was, and to infer details of the expansion, including the effective number of founders at the leading edge. These methods will be applied to data from several human populations in order to understand the recent history of population movement.

Public Health Relevance

The proposed research is intended to develop mathematical and statistical methods for analyzing DNA sequence data from individuals sampled from several closely related populations and to apply of those methods to data from human populations and their extinct close relatives, Neanderthals and Denisovans. One goal of the proposed research is to reveal past patterns of migration, admixture and range expansion in humans and to characterize the history of interactions of humans with Neanderthals and Denisovans. A second goal is to identify regions of the human genome that have been favored by recent natural selection since the separation from Neanderthals and Denisovans.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM040282-26A1
Application #
8696418
Study Section
Genetic Variation and Evolution Study Section (GVE)
Program Officer
Eckstrand, Irene A
Project Start
1988-09-01
Project End
2018-02-28
Budget Start
2014-04-01
Budget End
2015-02-28
Support Year
26
Fiscal Year
2014
Total Cost
$281,057
Indirect Cost
$91,057
Name
University of California Berkeley
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
124726725
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Theunert, Christoph; Racimo, Fernando; Slatkin, Montgomery (2017) Joint Estimation of Relatedness Coefficients and Allele Frequencies from Ancient Samples. Genetics 206:1025-1035
Theunert, Christoph; Slatkin, Montgomery (2017) Distinguishing recent admixture from ancestral population structure. Genome Biol Evol :
Schraiber, Joshua G; Evans, Steven N; Slatkin, Montgomery (2016) Bayesian Inference of Natural Selection from Allele Frequency Time Series. Genetics 203:493-511
Duforet-Frebourg, Nicolas; Slatkin, Montgomery (2016) Isolation-by-distance-and-time in a stepping-stone model. Theor Popul Biol 108:24-35
Slatkin, Montgomery; Racimo, Fernando (2016) Ancient DNA and human history. Proc Natl Acad Sci U S A 113:6380-7
Racimo, Fernando; Renaud, Gabriel; Slatkin, Montgomery (2016) Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans. PLoS Genet 12:e1005972
Slatkin, Montgomery (2016) Statistical methods for analyzing ancient DNA from hominins. Curr Opin Genet Dev 41:72-76
Racimo, Fernando (2016) Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. Genetics 202:733-50
Rogers, Rebekah L (2015) Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans. Mol Biol Evol 32:3064-78
Racimo, Fernando; Sankararaman, Sriram; Nielsen, Rasmus et al. (2015) Evidence for archaic adaptive introgression in humans. Nat Rev Genet 16:359-71

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