Maternal line analysis has usually been accomplished by amplifying the hypervariable regions of the mitochondrial DNA (mtDNA) control region (CR) using Sanger sequencing. However, this process is labor-intensive and underpowered for discovering the true diversity of a population when compared with whole-genome mtDNA approaches. With the introduction of next-generation sequencing in forensic and anthropology labs, we can now routinely sequence entire mtDNA genomes and uncover additional information on heteroplasmies, mtDNA genome structure, and the evolution of haplotypes and haplogroups among populations.
Simao et al. (1) undertook a project to do just that by sequencing the mtGenome of 105 unrelated males from Alto Parana, Paraguay, using the Precision ID mtDNA Whole Genome Panel and the Ion S5 System for next-generation sequencing. Two prior studies using the CR were small in sample size and focused on Indigenous populations. Dornelles et al. (2) analyzed 34 individuals from the Ayoreo ethnic group (western Paraguay) and found that 80% of the samples were from haplogroup C and the remainder were from haplogroup D. Schmitt et al. (3) sequenced 64 individuals from the Ache ethnic group (eastern Paraguay) to reveal that 90% were from haplogroup B and 10% were from haplogroup A. Both studies showed low haplotype diversity (<0.27).
In contrast, the whole-genome mtDNA analysis of Alto Paranans demonstrated that 84 samples had unique haplotypes. Only nine haploypes were shared by two individuals and one was shared by three individuals. Comparisons with the CR only revealed a different haplogroup in 26% of the samples (1).
Comparing all the data to other populations within South America, the authors found a large number of previously uncharacterized subclades. This high diversity may be the result of increased migration to Paraguay after the War of Triple Alliance (1865-1870), relocations by Paraguayans from other states, limited African influence during the slave trade or migration by male Brazilians who would have had higher admixture with African ancestry (1).
Next-gen sequencing technology using the automated workflow of the Applied Biosystems Precision ID System for human identification makes whole-genome analysis feasible, which results in higher resolution to help increase discrimination, as well as increased sensitivity. The small amplicon, highly multiplexed library preparation of the Precision ID mtDNA Whole Genome Panel makes it ideal for high-throughput applications, even with challenging samples.
1. Simão, Filipa et al. (2019) “The maternal inheritance of Alto Paraná revealed by full mitogenome sequences,” Forensic Science International: Genetics, 39, pp. 66 – 72.
2. Dornelles, C.L., Battilana, J., Fagundes, N.J.R., Freitas, L.B., Bonatto, S.L., Salzano, F.M. (2004) “Mitochondrial DNA and Alu insertions in a genetically peculiar population: the Ayoreo Indians of Bolivia and Paraguay,” Am. J. Hum. Biol. 16, pp. 479–488.
3. Schmitt, R., Bonatto, S.L., Freitas, L.B., Muschner, V.C., Hill, K., Hurtado, A.M., Salzano, F.M. (2004) “Extremely limited mitochondrial DNA variability among the Aché Natives of Paraguay,” Ann. Hum. Biol. 31, pp. 87–94.
For research, forensic or paternity use only. Not for use in diagnostic procedures.