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

Abstract

Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.

A genetic portrait of the South‐Eastern Carpathians based on autosomal short tandem repeats loci used in forensics

“…We then report estimates of the allele frequencies for well‐defined sub‐populations across the Carpathian Mountains, their fixation indexes, as well as their position in the genetic landscape of the Balkan Peninsula, as worked out by spatial methods specifically developed for genetic data. The results presented here fill an important gap in our previous data on the North‐Eastern Mediterranean (Messina et al, ), by expanding the geographic coverage of the 16‐loci dataset and thus providing a further opportunity to validate forensic STRs as useful population genetic markers.…”

“…Similar alleles were previously described in one or more of the STRBase (http://www.cstl.nist.gov/biotech/strbase/index.htm), ALLST*R (http://allstr.de/allstr/home.seam), or ref. (Messina et al, ).…”

“…Spatial principal component analysis (sPCA) was performed with the R package adegenet (Jombart, ), after pooling the original data here obtained with those reported by Messina et al (). A 12‐nearest neighbor network was used, and the top 2.5% scoring alleles on sPC 1 and 2 selected.…”

“…Following the same approach as in Messina et al () we generated reduced datasets by recoding the individual genotypes for the 8 alleles with the highest squared loadings on sPCs 1 and 2, respectively, against all the remaining alleles at the same locus. In order to visualize the estimated migration rates, we applied the program EEMS (Petkova, Novembre, & Stephens, ) to these reduced datasets.…”

“…While the above considerations should rule out forensic STRs for the study of intra‐continental gene geography, the interest in these markers for answering population genetics questions was reconsidered in recent studies (Messina et al, ). Indeed, it has been shown that, even on a scale of a few thousand kilometers, geographic arrangements of diversity can be captured if proper methods are used to extract the most informative loci and alleles.…”