Helena’s Many Daughters: More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample

Abstract

The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.

Complete Mitochondrial DNA Genome Variation in the Swedish Population

“…These Swedish mtDNA datasets showed lower HVS/CR haplotype diversity compared to those from other populations in Europe. With the analysis of the entire mitogenome, the number of unique haplotypes could increase dramatically, potentially to a 100% resolution of common HVS/CR haplotypes, as observed in other West Eurasian populations [7][8][9]18]. Studies have, moreover, concluded that there is no significant substructure within Sweden based on mtDNA HVS/CR and Y-chromosomal markers [16,17,19,20], which has also been confirmed with autosomal DNA studies [21,22].…”

“…The comparisons, which ignored all indels, were performed using two approaches for matching: literal (e.g., a Y only matches a Y at a position) and pattern (e.g., a Y matches a C or T at a position). Additionally, summary statistics were calculated based on the two HVS regions (HVS1 nps 16,024-16,365 and HVS2 nps 73-340), CR (16,024-16,569, 1-576), and the entire mitogenome (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)569).…”

“…The most common European HVS (nps 16,024-16,365, 73-340) haplotype "263G 315.1C" is observed in approximately 1 in every 15 West Eurasian individuals in the European DNA Profiling Group (EDNAP) mtDNA Population (EMPOP) database (v4/Release 13) [6]. The use of the entire CR (nps 16,024-16,569, 1-576) slightly improves the discrimination power for mtDNA analyses, but full mitogenome data are required to completely resolve common haplotypes [7][8][9].…”

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

“…NGS sequencing of the mtGenome has permitted improved resolution of the most common West Eurasian mtDNA control region haplotype [ 497 ]. Phylogenetic alignment and haplogroup classification have continued to be refined with new sequence information [ 498 ], and new assays have been developed to aid haplogroup classification [ 499 ].…”

The Revolution of Animal Genomics in Forensic Sciences

“…Nowadays, the extensive mtDNA typing of population data and the establishment of dedicated databases such as EMPOP (www.empop.org) provide as many as possible mitogenomes at a maximum level of resolution and quality. Phylogeographic investigations conducted on local populations distributed worldwide ( [61][62][63][64] as examples) constantly contribute toward the definition of reference population databases to be used at a microgeographic level. A branch of forensic genetics that frequently uses mitochondrial polymorphisms in conjunction with DNA barcoding is wildlife forensics, which deals with crimes perpetrated against protected species.…”