3D Interactive Multidimensional Scaling (MDS) for the Middle Eastern Populations

This model is a supplementary dataset for an article entitled “The Yemeni genetic structure revealed by the Y Chromosome STRs” and is fully described in the article (linked below in Related Materials).

Yemen, with its rich historical background and strategic geographical position at a major crossroads of trade and migration, offers an ideal setting for exploring population genetics. This study aimed to develop a Y-STR database for a Yemeni population and compare it with existing regional databases in the Middle East. For this investigation, buccal swabs were collected from 128 unrelated males. Genomic DNA was extracted using the QIAamp® DNA Mini Kit, and Y-chromosomal STR profiling was performed with the AmpFℓSTR® Yfiler™ PCR Amplification Kit to generate haplotype data across 17 Y-STR loci. The final dataset exhibited a haplotype diversity of 0.008 and a discrimination capacity of 0.95. Among the STR loci assessed, DYS458 emerged as the most polymorphic, displaying a gene diversity of 0.87 and accounting for the majority of microvariant alleles (62.5%). Additionally, haplogroup analysis (using the NevGen haplogroup predictor tool) revealed two predominant haplogroups within this Yemeni population: J1a (59.37%) and E1b1b (21.09%). Comparisons with 52 Middle Eastern populations (encompassing 5,568 individuals) through multidimensional scaling, phylogenetic assessments, admixture analyses, and ancestry variability evaluations collectively underscore the unique genetic landscape of Yemen. Overall, the combined findings indicate evidence of a potential founder effect within the Yemeni population. Taken together, these data not only enrich the forensic and population genetic understanding of the region but also emphasize Yemen’s pivotal role in illuminating migration and demographic processes in the Middle East.

Buccal swabs were collected from 128 unrelated male Yemeni students at the Faculty of Medicine and Health Sciences, Sana’a University, Yemen. All samples used in this study were obtained for the purpose of the research and ethical approval was granted by the ethical committee of the Faculty of Medicine and Health Sciences, Sana’a University, on 3rd of April 2007. Informed consent forms were completed by all participants and authors had no access to information that could identify individual participants during or after data collection. The data were collected in April 2007 and made accessible for research purposes in June 2007.