Worldwide FST Estimates Relative to Five Continental-Scale Populations

Abstract

We estimate the population genetics parameter (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. 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 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 is related to the variance of the multinomial-Dirichlet distribution for allele counts. Overall, we find low values, with posterior 97.5 percentiles when comparing a subpopulation with the most appropriate population, and even for inter-population comparisons we find . These are much smaller than single nucleotide polymorphism-based inter-continental 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 up to 3% in forensic calculations, which corresponds to some current practice.

Population-specific F values for forensic STR markers: A worldwide survey

“…From the perspective of a forensic scientist wanting to assign an F ST value for a broad geographic group, if an upper limit (the upper end of each whisker in Figure 4) was considered to be the most appropriate [3], then we would suggest values around 0.05 except for Native Americans and Inuits when the value is above 0.10. Rather than the upper limit, however, we have some preference for the median values (the center of each box in Figure 4), and these suggest values around 0.01–0.03 except for Native Americans and Inuits when the value are higher and more susceptible to the group or the world being the reference set.…”

“…Silva et al [1] made use of STR allele frequencies accessed from a then-online database strdna-db (Pamplona et al, [2]), while Steele et al [3] used data from people living in the United Kingdom (UK), or wishing to migrate to the UK on the basis of relatedness to a UK resident, as well as “reference” data collected by the UK Forensic Science Service. Both these papers provide useful reviews of the forensic uses of STR profiles and both describe the population genetic structure revealed by STR data.…”

“…Steele at al. [3] gave detailed analyses of the population structure quantity F ST that can be regarded as measuring the evolutionary relatedness between two individuals in the same population.…”

Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean

“…The overall Fst among the 41 location samples was 0.0022, a value which reveals the inability of forensic STRs to summarize differentiation into Fst, due to the large number of alleles, many of which with low frequencies [32], inflated intra-population variances [6, 7], and the mathematical constraint on the index [8]. Nevertheless, the departure of our value from the null (P<1E-4), showed that the sampling scheme may have the power to detect some kind of structuring.…”

“…However, these latter authors found low fixation indices, and suggested that, as far as these markers have been specifically selected to maximize the within-population (or between-subjects) variance, they carry a tiny proportion of information useful for between-population inferences. Additionally, it was suggested that the ethnic composition of population panels used in surveys with forensic and non-forensic loci may have resulted in lower fixation indexes in the former ones [7]. Recently, it was also shown that the widely used index Fst is mathematically constrained for loci with high heterozygosity, while statistics derived from multivariate methods are indeed able to extract ancestry information, reviving the value of loci for individual identification also in population identifiability, at least at the continental scale [8].…”