Current pool of ultimate collection of mitochondrial DNA from remnants of Kalash

Ethnogenetic analysis reveals the Bronze Age genetic affiliation of Yashkuns with West Eurasians

Focusing on the Yashkun population of Gilgit-Baltistan, an administrative territory in northern Pakistan, our study investigated mtDNA haplotypes as indicators of ancient gene flow and genetic diversity. Genomic DNA was extracted and evaluated for quality using agarose gel electrophoresis. The complete control region of mtDNA (nt 16024-576) was amplified via PCR, and sequencing was performed using the Big Dye Terminator Kit on an Applied Biosystems Genetic Analyzer. Sequence alignment and analysis were conducted using Geneious software and the Cambridge Reference Sequence (CRS). Haplotypes were classified into phylogenetic haplogroups with HaploGrep 2 and the Mito Tool platform, referencing PhyloTree version 17. The study identified considerable genetic diversity within the Yashkun population, with major macro-haplogroups H (29.47%), T (13.68%), and M (13.68%) representing West Eurasian, South Asian, and East & Southeast Asian lineages. The highest genetic affiliation was with West Eurasian haplogroups (73.68%), indicating significant gene flow from the West. The population's genetic distinctiveness was highlighted by the calculation of forensic genetic characteristics, such as power of discrimination (PD = 0.9975), genetic diversity (GD = 0.9865), and random match probability (RMP = 0.01349). The knowledge of the genetic makeup of the Yashkun population was further improved by the inference of phylogenetic links made possible by comparisons with other indigenous groups in Pakistan. These results attest to the reliability of mtDNA data for forensic applications such as ancestry tracking, individual identification, and additions to national forensic databases. The inclusion of mtDNA analysis in forensic science is strongly supported by this groundbreaking study on the Yashkun community, especially in areas like Pakistan with diverse genetic histories.

TPC2: From Blond Hair to Melanoma?

Two-pore channel 2 (TPC2) is expressed in endolysosomes throughout the human body, as well as in melanosomes of melanocytes. Melanocytes produce pigment, i.e., melanin, which determines hair and skin color but also protects from UV light. Extensive exposure to UV light is one of the major risk factors for the development of melanoma, which develops from pigment-producing cells, i.e., melanocytes. In recent years, several human TPC2 single nucleotide polymorphisms have been identified to increase the likelihood of carriers presenting with blond hair and hypopigmentation. These variants were all characterized as gain-of-function versions of TPC2. Vice versa, the loss of function of TPC2 increases melanin production and reduces cancer hallmarks such as proliferation, migration, invasion, tumor growth, and metastasis formation. The activity of TPC2 is controlled in a complex manner, with several endogenous ligands as well as a number of interacting proteins being involved. We will discuss here the role of TPC2 in pigmentation and its potential to impact melanoma development and progression and highlight recent findings on Rab7a as an enhancer of TPC2 activity.

A comprehensive review of HVS-I mitochondrial DNA variation of 19 Iranian populations

Iran is located along the Central Asian corridor, a natural artery that has served as a cross-continental route since the first anatomically modern human populations migrated out of Africa. We compiled and reanalyzed the HVS-I (hypervariable segment-I) of 3840 mitochondrial DNA (mtDNA) sequences from 19 Iranian populations and from 26 groups from adjacent countries to give a comprehensive review of the maternal genetic variation and investigate the impact of historical events and cultural factors on the maternal genetic structure of modern Iranians. We conclude that Iranians have a high level of genetic diversity. Thirty-six haplogroups were observed in Iran's populations, and most of them belong to widespread West-Eurasian haplogroups, such as H, HV, J, N, T, and U. In contrast, the predominant haplogroups observed in most of the adjacent countries studied here are H, M, D, R, U, and C haplogroups. Using principal component analysis, clustering, and genetic distance-based calculations, we estimated moderate genetic relationships between Iranian and other Eurasian groups. Further, analyses of molecular variance and comparing geographic and genetic structures indicate that mtDNA HVS-I sequence diversity does not exhibit any sharp geographic structure in the country. Barring a few from some culturally distinct and naturally separated minorities, most Iranian populations have a homogenous maternal genetic structure.

Genetic diversity and forensic application of Y-filer STRs in four major ethnic groups of Pakistan

17 Y-chromosomal STRs which are part of the Yfiler Amplification Kit were investigated in 493 unrelated Pakistani individuals belonging to the Punjabi, Sindhi, Baloch, and Pathan ethnic groups. We have assessed the forensic parameters and population genetic structure for each group. Among the 493 unrelated individuals from four ethnic groups (128 Baloch, 122 Pathan, 108 Punjabi, and 135 Sindhi), 82 haplotypes were observed with haplotype diversity (HD) of 0.9906 in Baloch, 102 haplotypes with HD value of 0.9957 in Pathans, 80 haplotypes with HD value of 0.9924 in Punjabi, and 105 haplotypes with HD value of 0.9945 in the Sindhi population. The overall gene diversity for Baloch, Pathan, Punjabi, and Sindhi populations was 0.6367, 0.6479, 0.6657, and 0.6112, respectively. The results had shown us that Pakistani populations do not have a unique set of genes but share the genetic affinity with regional (Central Asia and Northern India) populations. The observed low gene diversity (heterozygosity) values may be because of endogamy trends and this observation is equally supported by the results of forensic parameters which are mostly static across 4 combinations (minimal STRs, extended 11 Y-STRs, Powerplex 12 Y System, and Yfiler 17 Y-STRs) of STRs in these four populations.