Human Neutral Genetic Variation and Forensic STR Data

Abstract

The forensic genetics field is generating extensive population data on polymorphism of short tandem repeats (STR) markers in globally distributed samples. In this study we explored and quantified the informative power of these datasets to address issues related to human evolution and diversity, by using two online resources: an allele frequency dataset representing 141 populations summing up to almost 26 thousand individuals; a genotype dataset consisting of 42 populations and more than 11 thousand individuals. We show that the genetic relationships between populations based on forensic STRs are best explained by geography, as observed when analysing other worldwide datasets generated specifically to study human diversity. However, the global level of genetic differentiation between populations (as measured by a fixation index) is about half the value estimated with those other datasets, which contain a much higher number of markers but much less individuals. We suggest that the main factor explaining this difference is an ascertainment bias in forensics data resulting from the choice of markers for individual identification. We show that this choice results in average low variance of heterozygosity across world regions, and hence in low differentiation among populations. Thus, the forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.

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.…”

“…Rowold and Herrera [5] used five forensic STRs and obtained phylogenetic relationships of worldwide populations consistent with other markers. Silva et al [6] detected a progressive reduction of diversity with increasing distance from Eastern Africa, a signature of the serial founder effect which accompanied the spread of modern humans out of Africa and beyond. 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.…”

Grazing history influences biodiversity: a case study on ground-dwelling arachnids (Arachnida: Araneae, Opiliones) in the Natural Park of Alpi Marittime (NW Italy)

“…Second, we observed random spatial patterns of relatedness among individuals, which may indicate no restriction in gene flow across a few kilometers (see also Smouse and Peakall 1999;Peakall et al 2003;Chybicki 2017). Third, the population structure, as inferred from STRU CTU RE, was only partially consistent with geography, nevertheless STRU CTU RE clustering may be biased due to a low number of loci analyzed (Silva et al 2012). The observed departures from Hardy-Weinberg equilibrium could thus be rather attributed to substantial inbreeding (F i null avg .…”

The Orientalisation of North Africa: New hints from the study of autosomal STRs in an Arab population

“…They are quite able to detect strong genetic structure, as we have observed here with the clear differentiation between Sub-Saharan African, East Asian and European populations, for instance. However, in comparison to panels of STRs generated specifically to study diversity of human populations, forensic STRs underestimate levels of structure, thus providing lower differentiations among populations (Silva et al, 2012).…”

“…Previous studies have provided important contributions to understand the genetic structure of North African populations, using various genetic markers, such as mitochondrial DNA (mtDNA) (Fadhlaoui-Zid et al, 2004;Frigi et al, 2006aFrigi et al, , 2010Coudray et al, 2009;Ottoni et al, 2010;Bekada et al, 2015), Y chromosome Short Tandem Repeats (STRs) (Fadhlaoui-Zid et al, 2011, 2013Frigi et al, 2006b;Arredi et al, 2004;Bekada et al, 2015), Single Nucleotide Polymorphisms (SNP), (Henn et al, 2012, Botigué et al, 2013Haber et al, 2013), Alu insertions (Gonzalez-Pérez et al, 2003;Ennafaa et al, 2006;Frigi et al, 2011) and autosomal STRs (Bosch et al, 2001;Cherni et al, 2005a;Coudray et al, 2007aCoudray et al, , 2007bCoudray et al, , 2007cElOssmani et al, 2007ElOssmani et al, , 2009ElOssmani et al, , 2010Khodjet-El-Khil et al, 2008, 2012Gaibar et al, 2012).…”