Table of Contents
Haplogroup Classification in Mitochondrial DNA: Insights from Pakistani Populations
Last Updated: August 12, 2025
Introduction
Every person’s mitochondrial DNA tells a story — a genetic path tracing back thousands of years to ancient ancestors. The key to unlocking these stories lies in haplogroup classification, a process that organizes mtDNA sequences into distinct genetic branches.
In Pakistan, haplogroup classification of the Makrani and Kalashi populations has revealed fascinating patterns of ancestry, migration, and population history. This post examines how these haplogroups were identified, what they mean, and why they matter in both anthropology and forensic science.
Thesis Excerpt & Analysis
“The sequence data obtained was compared with the Cambridge Reference Sequence (CRS) and the haplogroups were assigned based on PhyloTree build 15… in cases of ambiguity, the haplogroup was designated at the highest level of certainty” (p. 54).
How Haplogroup Classification Works
- Sequence Alignment: Compare mtDNA sequences to a standard reference (CRS).
- Mutation Identification: Note variations in hypervariable regions.
- Phylogenetic Mapping: Place sequences into branches of the human mtDNA tree using databases like PhyloTree.
- Haplogroup Assignment: Assign the lineage based on matching mutation patterns.
Makrani Haplogroup Distribution
“A total of 27 haplogroups were identified in Makrani population with a majority of L haplogroups of African origin, followed by M and N haplogroups of South and West Eurasian origin” (p. 70).
- L haplogroups: Strong African ancestry component.
- M haplogroups: South Asian and East Asian links.
- N haplogroups: European and Middle Eastern maternal lineages.
Kalashi Haplogroup Distribution
“In Kalashi population, 7 haplogroups were identified with an overwhelming majority of West Eurasian lineages, particularly haplogroup H” (p. 73).
- H haplogroup: Widely found in Europe, linked to post-Ice Age expansions.
- Smaller representation of J, HV, and U haplogroups, all West Eurasian.
Significance of Haplogroup Classification
- Anthropology: Traces population origins and migration routes.
- Forensics: Narrows down possible matches by linking to specific maternal lineage groups.
- Genetics Research: Helps identify medically relevant mutations tied to specific lineages.
Limitations and Future Directions
“Tentatively assigned haplogroup named ‘M-154-194’ could not be confidently classified… further complete mitogenome sequencing is required” (p. ii).
- Some sequences remain unclassified without deeper genomic data.
- Future research will likely uncover new sub-haplogroups.
Conclusion
Haplogroup classification is more than a technical step in DNA analysis — it is the foundation for understanding how people are connected across time and space. The Makrani and Kalashi populations illustrate how diverse or homogeneous haplogroup patterns can reflect centuries of migration, isolation, and cultural history.
Disclaimer
Disclaimer: Some sentences have been lightly edited for SEO and readability. For the full, original research, please refer to the complete thesis PDF linked in the section above.
Source & Citations
Thesis Title: Genetic Characterization of Mitochondrial DNA in Makrani and Kalashi Population from Pakistan
Researcher: Muhammad Hassan Siddiqi
Guide (Supervisor): Prof. Dr. Tanveer Akhtar
University: University of the Punjab, Lahore, Pakistan
Year of Compilation: 2014
Excerpt Page Numbers: ii, 54, 70–74
Author Bio
Muhammad Hassan Siddiqi, PhD, is a zoologist and geneticist with expertise in human mitochondrial DNA, haplogroup analysis, and forensic anthropology. His research has advanced understanding of South Asian genetic history.
Which haplogroup discovery do you find more intriguing — the Makrani’s diverse African and Eurasian mix or the Kalashi’s dominant West Eurasian lineage? Share your thoughts below.
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