Problems in Mitochondrial DNA forensics: while interpreting length heteroplasmy conundrum of various Sindhi and Baluchi ethnic groups of Pakistan

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.

Forensic use of human mitochondrial DNA: A review

In forensics, genetic human identification is generally achieved by nuclear STR DNA typing. However, forensic samples often yield DNA in exiguous quantity and low quality, impairing the generation of conclusive DNA profiles by STR typing. In such cases, mitochondrial DNA (mtDNA) can be used as an alternative solution in forensic human identification. The high copy number, small circular DNA, high mutation rate, maternal inheritance, and absence of recombination are mtDNA's key features in forensics. In this work, we review mtDNA characteristics, forensic applications, sequencing methodologies and present some relevant examples in the forensic science literature.

Portunus pelagicus mtDNA heteroplasmy inheritance and its effect on the use of mtCR and mtCOI sequence data

Mitochondrial DNA (mtDNA) sequences, especially mitochondrial control region (mtCR) and mitochondrial cytochrome c oxidase subunit I (mtCOI), have been widely used in population and evolutionary genetic analyses of metazoan. The presence of mtDNA heteroplasmy - a mixture of mtDNA haplotypes - possibly affects these analyses. This study aimed to reveal mtDNA heteroplasmy in mtCR, mtCOI, and mtND2 (mitochondrial NADH dehydrogenase subunit 2) of Portunus pelagicus, and examine its effect on the use of mtCR and mtCOI sequences. The screening result showed that the probability of observing mtDNA heteroplasmy was approximately 8%. Across the three targeted regions, 92 heteroplasmic variants were observed from seven samples comprising three mothers and four offspring. Most inherited heteroplasmy presented transition and silence mutation. By comparing the proportion of shared variants among maternal relatives to that among non-relatives, the result suggested that most heteroplasmic variants observed in an individual are inherited. Statistical analyses carried out on the inter-generational differences suggested that random drift and purifying selection play roles in determining the offspring's heteroplasmy level. The size of the random shift varies according to the location of variants and the mothers. The phylogenetic analysis showed that the presence of mtDNA heteroplasmy in mtCR and mtCOI does not affect familial and species identification, respectively. This study firstly reported the mtDNA heteroplasmy in P. pelagicus, its inheritance pattern, and its effect on the use of mtDNA sequence data. This basic knowledge would be useful for the study based on mtDNA sequence data, especially in other invertebrates.

Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan

To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.