Steele, CD; Court, DS; Balding, DJ; (2014) Worldwide F-ST Estimates Relative to Five Continental-Scale Populations. ANNALS OF HUMAN GENETICS , 78 (6) 468 - 477. 10.1111/ahg.12081.

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Abstract

We estimate the population genetics parameter inline image (also referred to as the fixation index) from short tandem repeat (STR) allele frequencies, comparing many worldwide human subpopulations at approximately the national level with continental-scale populations. inline image is commonly used to measure population differentiation, and is important in forensic DNA analysis to account for remote shared ancestry between a suspect and an alternative source of the DNA. We estimate inline image comparing subpopulations with a hypothetical ancestral population, which is the approach most widely used in population genetics, and also compare a subpopulation with a sampled reference population, which is more appropriate for forensic applications. Both estimation methods are likelihood-based, in which inline image is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low inline image values, with posterior 97.5 percentiles inline image when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find inline image inline image. These are much smaller than single nucleotide polymorphism-based inter-continental inline image estimates, and are also about half the magnitude of STR-based estimates from population genetics surveys that focus on distinct ethnic groups rather than a general population. Our findings support the use of inline image up to 3% in forensic calculations, which corresponds to some current practice.

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