Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers

Abstract

Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

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

“…We endorse the concerns thoroughly discussed [8], which emerge from this perhaps unwanted property of such markers. Mathematically, the degree of population identifiability may have a non-null impact on calculations of the posterior probability of individual assignment.…”

“…Some loci contributed to the same sPC with more than one allele, a not unexpected finding in view of the intrinsic negative correlation between the frequencies of alternative alleles at the same locus. Finally, only in 9 out of 16 loci the most frequent allele emerged, confirming that a relevant spatial signal was often due to alleles that contribute only marginally to the overall variance [8]. These observations suggested that some loci, and some of their alleles, convey a clearer signal of spatial structuring, and one or more reduced datasets can be obtained, which could retain most of the geographic information but with an abated background noise.…”

“…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.…”

“…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]. …”

Better together: Thinking anthropologically about genetics

“…Increasing interest within both the scientific and public communities in the ancestral origins of modern humans has led to significant advances in how we seek to understand the genetic history of global populations and their members using a variety of data types (Creanza et al, 2015;Hellenthal et al, 2014;Henn, CavalliSforza, & Feldman, 2012;Manica, Amos, Balloux, & Hanihara, 2007). In recent years, focus in human genetics has shifted accordingly toward large-scale genomic analyses of complex population histories, including ancient and forensic samples, and previously underserved populations (Algee-Hewitt, Edge, Kim, Li, & Rosenberg, 2016;Moreno-Estrada et al, 2014;Raghavan et al, 2015). With this emphasis on human history and the expansion of research potential that genomics has brought to the fundamental questions of anthropology, genetic analyses are now approximating the kinds of information that anthropologists have historically estimated from visible or measurable traits.…”