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Ahlawat B, Kumar L, Cherian PJ, Sehrawat JS, Rai N, Thangaraj K. Deciphering the West Eurasian Genetic Footprints in Ancient South India. Genes (Basel) 2023; 14:genes14050963. [PMID: 37239323 DOI: 10.3390/genes14050963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Since 2006, Pattanam coastal village of the Ernakulam District in Kerala, India, has witnessed multi-disciplinary archaeological investigations in collaboration with leading research institutions across the world. The results confirm that the Pattanam site could be an integral part of the lost ancient port of Muziris, which, as per the material evidence from Pattanam and its contemporary sites, played an important role in the transoceanic exchanges between 100 BCE (Before Common Era) and 300 CE (Common Era). So far, the material evidence with direct provenance to the maritime exchanges related to ancient cultures of the Mediterranean, West Asian, Red Sea, African, and Asian regions have been identified at Pattanam. However, the genetic evidence supporting the impact of multiple cultures or their admixing is still missing for this important archaeological site of South India. Hence, in the current study, we tried to infer the genetic composition of the skeletal remains excavated from the site in a broader context of South Asian and worldwide maternal affinity. We applied the MassArray-based genotyping approach of mitochondrial makers and observed that ancient samples of Pattanam represent a mixed maternal ancestry pattern of both the West Eurasian ancestry and the South Asian ancestry. We observed a high frequency of West Eurasian haplogroups (T, JT, and HV) and South Asian-specific mitochondrial haplogroups (M2a, M3a, R5, and M6). The findings are consistent with the previously published and ongoing archaeological excavations, in which material remains from over three dozen of sites across the Indian Ocean, Red Sea, and Mediterranean littoral regions have been unearthed. This study confirms that people belonging to multiple cultural and linguistic backgrounds have migrated, probably settled, and eventually died on the South-western coast of India.
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Affiliation(s)
- Bhavna Ahlawat
- Department of Anthropology, Panjab University, Chandigarh 160014, India
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Parayil John Cherian
- PAMA Institute for the Advancement of Transdisciplinary Archaeological Sciences, Pattanam Archaeological Site, Ernakulam 683522, India
- Kerala Council for Historical Research & Director Pattanam Excavations, Thiruvananthapuram 695003, India
| | | | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
- Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad 500007, India
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Dalal V, Pasupuleti N, Chaubey G, Rai N, Shinde V. Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide. Genes (Basel) 2023; 14:479. [PMID: 36833406 PMCID: PMC9956214 DOI: 10.3390/genes14020479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.
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Affiliation(s)
- Vasundhra Dalal
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226007, Uttar Pradesh, India
| | - Vasant Shinde
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
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Sehrawat JS, Agrawal S, Sankhyan D, Singh M, Kumar S, Prakash S, Rajpal R, Chaubey G, Thangaraj K, Rai N. Pinpointing the Geographic Origin of 165-Year-Old Human Skeletal Remains Found in Punjab, India: Evidence From Mitochondrial DNA and Stable Isotope Analysis. Front Genet 2022; 13:813934. [PMID: 35571044 PMCID: PMC9095824 DOI: 10.3389/fgene.2022.813934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
In 2014, 157 years after the Sepoy Mutiny of 1857, several unidentified human skeletons were discovered in an abandoned well at Ajnala, Punjab. The most prevailing hypothesis suggested them as Indian soldiers who mutinied during the Indian uprising of 1857. However, there is an intense debate on their geographic affinity. Therefore, to pinpoint their area of origin, we have successfully isolated DNA from cementum-rich material of 50 good-quality random teeth samples and analyzed mtDNA haplogroups. In addition to that, we analyzed 85 individuals for oxygen isotopes (δ18O values). The mtDNA haplogroup distribution and clustering pattern rejected the local ancestry and indicated their genetic link with the populations living east of Punjab. In addition, the oxygen isotope analysis (δ18O values) from archaeological skeletal remains corroborated the molecular data and suggested the closest possible geographical affinity of these skeletal remains toward the eastern part of India, largely covering the Gangetic plain region. The data generated from this study are expected to expand our understanding of the ancestry and population affinity of martyr soldiers.
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Affiliation(s)
- J S Sehrawat
- Department of Anthropology, Panjab University, Chandigarh, India
| | | | - Deeksha Sankhyan
- Department of Anthropology, Panjab University, Chandigarh, India
| | - Monika Singh
- Department of Anthropology, Panjab University, Chandigarh, India
| | - Sachin Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Satya Prakash
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Gyaneshwer Chaubey
- Cytogenetic Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
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Chaubey G, Ayub Q, Rai N, Prakash S, Mushrif-Tripathy V, Mezzavilla M, Pathak AK, Tamang R, Firasat S, Reidla M, Karmin M, Rani DS, Reddy AG, Parik J, Metspalu E, Rootsi S, Dalal K, Khaliq S, Mehdi SQ, Singh L, Metspalu M, Kivisild T, Tyler-Smith C, Villems R, Thangaraj K. "Like sugar in milk": reconstructing the genetic history of the Parsi population. Genome Biol 2017; 18:110. [PMID: 28615043 PMCID: PMC5470188 DOI: 10.1186/s13059-017-1244-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/23/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest.
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Affiliation(s)
- Gyaneshwer Chaubey
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Niraj Rai
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Present address: Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Satya Prakash
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Veena Mushrif-Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra, 411006, India
| | - Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ajai Kumar Pathak
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, 700073, India
| | - Sadaf Firasat
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan
| | - Maere Reidla
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Monika Karmin
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia.,Department of Psychology, University of Auckland, Auckland, 1142, New Zealand
| | - Deepa Selvi Rani
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Alla G Reddy
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Jüri Parik
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Ene Metspalu
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Siiri Rootsi
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia
| | - Kurush Dalal
- Centre for Archaeology (CfA), Centre for Extra Mural Studies (CEMS) University of Mumbai (Kalina Campus) Vidyanagri, Santacruz E Mumbai, 400098, India
| | - Shagufta Khaliq
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore, 54000, Pakistan
| | - Syed Qasim Mehdi
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan
| | - Lalji Singh
- Genome foundation, C/o Prasad Hospital, Nacharam, Hyderabad, 500076, India
| | - Mait Metspalu
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
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Jain S, Rai N, Kumar G, Pruthi PA, Thangaraj K, Bajpai S, Pruthi V. Ancient DNA Reveals Late Pleistocene Existence of Ostriches in Indian Sub-Continent. PLoS One 2017; 12:e0164823. [PMID: 28273082 PMCID: PMC5342186 DOI: 10.1371/journal.pone.0164823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/01/2016] [Indexed: 11/18/2022] Open
Abstract
Ancient DNA (aDNA) analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating) using confocal laser scanning microscopy (CLSM). DNA was isolated from five eggshell fragments and a 43 base pair (bp) sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples. Phylogenetic analysis of the DNA sequence revealed a 92% identity of the fossil eggshells to Struthio camelus and their position basal to other palaeognaths, consistent with the vicariant speciation model. Our study provides the first molecular evidence for the presence of ostriches in India, complementing the continental drift theory of biogeographical movement of ostriches in India, and opening up a new window into the evolutionary history of ratites.
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Affiliation(s)
- Sonal Jain
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
- * E-mail:
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Giriraj Kumar
- Dayalbagh Educational Institute, Dayalbagh, Agra, UP, India
| | - Parul Aggarwal Pruthi
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | | | - Sunil Bajpai
- Department of Earth Sciences, Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Vikas Pruthi
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, India
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