Population of Northern Portugal: Study of Genetic Diversity and Forensic Parameters of 26 Y-STR Markers

[Tautalus]

Abstract

Background: Short tandem repeats (STRs) are highly variable sequences present along the human genome, including the Y-chromosome. Y-STRs are exclusive to males, and the haplotypes they define are informative. Objectives: Twenty-six Y-STR loci were genotyped in 252 males from Northern Portugal to characterise Y-chromosome genetic variation using the Investigator Argus Y28 QS Kit. Methods: The kit mentioned was used to amplify male DNA samples, and capillary electrophoresis was used to analyze the fragments. Forensic parameters and haplotype diversity were computed, and samples’ haplogroups were predicted. A multidimensional scaling (MDS) plot was used to graphically represent the RST genetic distances, including reference populations. Results: A total of 250 different haplotypes were observed, including 248 unique ones, yielding a very high haplotype diversity (HD = 0.999) and discriminatory power (DP = 0.992). Haplogroup analysis indicated a predominance of R1b (58.7%), followed by E1b1b, I and J, pointing to a population history shaped by Mediterranean and North African gene flow. Comparative analysis between Portugal and 5 other populations showed greater genetic affinity with Spain and Italy, while revealing marked differentiation from Greece, Morocco, and former Portuguese colonies. Conclusions: The results confirm that the Northern Portuguese Population exhibits high Y-STR variability and robust forensic resolution. The dataset was submitted to the YHRD database, enhancing the representation of the Portuguese population and underscoring the value of the 26 locus panel for applications in forensic science, genealogy, and population genetics.
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https://pmc.ncbi.nlm.nih.gov/articles/PMC12841522/​

Haplogroup frequencies in the Northern Portuguese population.

 

[MOESAN]

weak resolution...

 

[Tautalus]

Yes. NevGen Y-DNA Haplogroup Predictor STR-based prediction has limitations.
They say in the paper that “It is important to note that haplogroup inference in this study is based on Y-STR and the NevGen predictor. STR-based assignments are uncertain and may lead to misclassification. The historical interpretations presented here should be regarded as broad population-level tendencies consistent with prior studies, rather than definitive phylogenetic conclusions, and are presented only in the context of well-established Iberian paternal lineages. While this approach is informative at a broad population level, STR-based inference does not replace SNP-defined haplogroup determination. Future studies incorporating Y-SNP typing will be necessary to refine phylogenetic resolution and strengthen historical inference.”​

 

[—BoNe—]

The study looks like it’s from 2005; they’ve scanned STRs as if the SNPs weren’t already documented. I think it’s by far the most anachronistic study I’ve seen to date.

There are many studies like this whose purpose is unclear, and I don’t think even the authors really know what they were aiming for. I doubt any ordinary reader could extract much information from them. The study would have been radically different if they had applied SNP filtering instead of STRs.

STR analysis is the very first step before assigning the SNPs.

Since the SNPs are already catalogued, they could have identified very deep clades using just the STRs, but they don’t—for God knows what reason. I think some publicly funded researchers live in a parallel universe.

If they’ve made the supplementary data public, then by running it through a program fed with phylogenetic trees, like YFull, all the terminal clades would appear.