PT - JOURNAL ARTICLE
AU - Peter, Benjamin M.
TI - Admixture, Population Structure, and <em>F</em>-Statistics
AID - 10.1534/genetics.115.183913
DP - 2016 Apr 01
TA - Genetics
PG - 1485--1501
VI - 202
IP - 4
4099 - http://www.genetics.org/content/202/4/1485.short
4100 - http://www.genetics.org/content/202/4/1485.full
SO - Genetics2016 Apr 01; 202
AB - Many questions about human genetic history can be addressed by examining the patterns of shared genetic variation between sets of populations. A useful methodological framework for this purpose is F-statistics that measure shared genetic drift between sets of two, three, and four populations and can be used to test simple and complex hypotheses about admixture between populations. This article provides context from phylogenetic and population genetic theory. I review how F-statistics can be interpreted as branch lengths or paths and derive new interpretations, using coalescent theory. I further show that the admixture tests can be interpreted as testing general properties of phylogenies, allowing extension of some ideas applications to arbitrary phylogenetic trees. The new results are used to investigate the behavior of the statistics under different models of population structure and show how population substructure complicates inference. The results lead to simplified estimators in many cases, and I recommend to replace F3 with the average number of pairwise differences for estimating population divergence.