Y-STR haplotype diversity in Eritrean and Sudanese populations

Introduction: East Africa has been in the spotlight of paleoanthropological investigations for its role as a potential cradle of humanity and as a gateway out of Africa. Y chromosome single nucleotide polymorphisms (SNPs) and mitochondrial DNA genotyping of East African populations complement this notion and further demonstrate the high effective population size and genetic diversity of East African populations to attest to the antiquity of the populations of the region. This study aims to investigate the genetic diversity of representative Eritrean and Sudanese samples via Y chromosome short tandem repeats (STRs) and SNP analysis. Materials and methods: In this study, Y chromosome-specific STR (Y-STR) and Y chromosome SNP (Y-SNP) genotyping and haplogroup prediction were performed on 95 unrelated male samples from Eritrea and Sudan in an effort to understand the genetic history of East Africa. Results: Population differentiation analysis of 95 samples revealed 90 unique haplotypes. Further population differentiation analysis of 562 samples generated 451 haplotypes (395 unique and 56 shared haplotypes), and most of the shared haplotypes were found in individuals of the same population group. Pooled samples at the 17 and 12 Y-STR levels were used to give our analysis a regional and global context. Conclusions: The overall analysis revealed the high genetic diversity of East African populations. The clustering of Y-STRs along their respective haplogroups implies the necessity of future joint Y-SNP and Y-STR data analysis on populations of the region to further clarify the association between the two Y chromosome markers and their implications for forensics and population differentiation studies in the region.