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Fernando AS, Wanninayaka A, Dewage D, Karunanayake EH, Rai N, Somadeva R, Tennekoon KH, Ranasinghe R. The mitochondrial genomes of two Pre-historic Hunter Gatherers in Sri Lanka. J Hum Genet 2023; 68:103-105. [PMID: 36450887 DOI: 10.1038/s10038-022-01099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Sri Lanka is an island in the Indian Ocean connected by the sea routes of the Western and Eastern worlds. Although settlements of anatomically modern humans date back to 48,000 years, to date there is no genetic information on pre-historic individuals in Sri Lanka. We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese. Both haplogroups are Indian derived and observed in the South Asian region and rarely outside the region.
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Affiliation(s)
- A S Fernando
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - A Wanninayaka
- Postgraduate Institute of Archeology, University of Kelaniya, Kelaniya, Sri Lanka
| | - D Dewage
- Postgraduate Institute of Archeology, University of Kelaniya, Kelaniya, Sri Lanka
| | - E H Karunanayake
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - N Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - R Somadeva
- Postgraduate Institute of Archeology, University of Kelaniya, Kelaniya, Sri Lanka
| | - K H Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - R Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka.
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Sikdar M. Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India. Am J Hum Biol 2022; 35:e23851. [PMID: 36571462 DOI: 10.1002/ajhb.23851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVES Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. METHODS To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North-western India have been sequenced. RESULTS Interestingly, three novel sub-clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. CONCLUSION The haplotype-based analysis suggests that the Kayastha population shares genetic affinities with the Indo-European and Sino-Tibetan populations found in the trans-Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub-continent. Both mtDNA and Y-chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations.
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Affiliation(s)
- Mithun Sikdar
- DNA Laboratory Unit, Anthropological Survey of India, Southern Regional Center, Mysore, India
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Agrawal P, Katragadda S, Hariharan AK, Raghavendrachar VG, Agarwal A, Dayalu R, Awasthy D, Sharma SC, Sivasamy YK, Lakshmana P, Shanmugam A, Veeramachaneni V, Gupta V, Vani BP, Subaiya L, Syamala TS, Hariharan R, Chandru V, Bloom DE. Validation of whole genome sequencing from dried blood spots. BMC Med Genomics 2021; 14:110. [PMID: 33879142 PMCID: PMC8056537 DOI: 10.1186/s12920-021-00951-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dried blood spots (DBS) are a relatively inexpensive source of nucleic acids and are easy to collect, transport, and store in large-scale field surveys, especially in resource-limited settings. However, their performance in whole-genome sequencing (WGS) relative to that of venous blood DNA has not been analyzed for various downstream applications. METHODS This study compares the WGS performance of DBS paired with venous blood samples collected from 12 subjects. RESULTS Results of standard quality checks of coverage, base quality, and mapping quality were found to be near identical between DBS and venous blood. Concordance for single-nucleotide variants, insertions and deletions, and copy number variants was high between these two sample types. Additionally, downstream analyses typical of population-based studies were performed, such as mitochondrial heteroplasmy detection, haplotype analysis, mitochondrial copy number changes, and determination of telomere lengths. The absolute mitochondrial copy number values were higher for DBS than for venous blood, though the trend in sample-to-sample variation was similar between DBS and blood. Telomere length estimates in most DBS samples were on par with those from venous blood. CONCLUSION DBS samples can serve as a robust and feasible alternative to venous blood for studies requiring WGS analysis.
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Affiliation(s)
- Pooja Agrawal
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Shanmukh Katragadda
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Arun K Hariharan
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | | | - Arunika Agarwal
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, 02115, USA
| | - Rashmi Dayalu
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, 02115, USA
| | - Disha Awasthy
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Sanjay C Sharma
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Yasodha Kannan Sivasamy
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - P Lakshmana
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Ashwini Shanmugam
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Vamsi Veeramachaneni
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Vaijayanti Gupta
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - B P Vani
- The Institute for Social and Economic Change, Dr. VKRV Rao Road, Teachers Colony, Nagarabhavi, Bangalore, Karnataka, 560072, India
| | - Lekha Subaiya
- The Institute for Social and Economic Change, Dr. VKRV Rao Road, Teachers Colony, Nagarabhavi, Bangalore, Karnataka, 560072, India
| | - T S Syamala
- The Institute for Social and Economic Change, Dr. VKRV Rao Road, Teachers Colony, Nagarabhavi, Bangalore, Karnataka, 560072, India
| | - Ramesh Hariharan
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India
| | - Vijay Chandru
- Strand Life Sciences Pvt. Ltd., Ground Floor, UAS Alumni Association Building, Veterinary College Campus, Bellary Road, Bangalore, Karnataka, 560024, India.
- Centre for BioSystems Science and Engineering, 3rd Floor, C Wing, Biological Sciences Building, Indian Institute of Science, Bangalore, 560012, India.
| | - David E Bloom
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, 02115, USA.
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Mumtaz MN, Ihsan H, Aziz S, Hizbullah, Afridi SG, Shams S, Khan A. The genetic composition of Shina population from Gilgit-Baltistan, Pakistan based on mtDNA analyses. Mitochondrial DNA B Resour 2019; 4:3802-3808. [PMID: 33366198 PMCID: PMC7710323 DOI: 10.1080/23802359.2019.1682474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/13/2019] [Indexed: 02/02/2023] Open
Abstract
The present study aimed to gain insight into the genetic origin of the Shina population from Gilgit-Baltistan, Pakistan. We partially performed the mitochondrial DNA (mtDNA) control region of healthy unrelated individuals of Shina tribe residing in the remote area of Gilgit-Baltistan to investigate their maternal lineages. The present study is the first report about Shina's genetic structure, origin, and relationship with the surrounding north-western Pakistani population. The mtDNA sequences of the Shina samples were compared with the revised Cambridge Reference Sequence (rCRS) and the HVR-1 D-loop region was covered. The comparison with rCRS identified overall 38 haplotypes and 08 haplogroups for Shina samples. Among these haplotypes, 18 were shared by more than one individual of the Shina tribe. The obtained mtDNA sequences of Shina were compared with surrounding north-western Pakistani population groups, i.e. Kho, Kashmiri, and Pathan. The genetic diversity (i.e. 1.0424) and power of discrimination (i.e. 0.9266) of the Shina was found equivalent to surrounding north-western groups. The haplogroups frequencies, phylogenetic tree and network analysis identified the west Eurasian ancestral origin of Shina group with nearby maternal ancestral relationships with the Kashmiri population. However, no close genetic relationship of Shina was depicted with nearby residing Kho population group.
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Affiliation(s)
- Mah Noor Mumtaz
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Haleema Ihsan
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Aziz
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Hizbullah
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Sahib Gul Afridi
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University, Mardan23200, Khyber Pakhtunkhwa, Pakistan
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Mitochondrial DNA sequencing reveals association of variants and haplogroup M33a2'3 with High altitude pulmonary edema susceptibility in Indian male lowlanders. Sci Rep 2019; 9:10975. [PMID: 31358833 PMCID: PMC6662842 DOI: 10.1038/s41598-019-47500-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 07/18/2019] [Indexed: 12/29/2022] Open
Abstract
High Altitude Pulmonary Edema (HAPE) is a threatening disorder caused due to acute exposure to high altitude above 3000 m. Apart from multiple factors involved, the genetic factors also play an important function in the pathogenesis of HAPE. This study aims to evaluate the role of mtDNA polymorphism and their association with haplogroup in understanding the etiology of HAPE. In this study, all the HAPE susceptible and acclimatized control subjects could be classified into nine haplogroups pertaining mostly to Macrohaplogroup M and U. The frequency of haplogroup M was significantly higher in HAPE susceptibles whereas the haplogroup M33a2'3 was found only in HAPE susceptibles. The variant G4491A and A4944G of MT-ND2, A14002G of MT-ND5, and C8562T of MT-ATP8, were definition site of haplogroup M33a2'3. The frequency of A10398G of MT-ND3, A8701G of MT-ATP6 and C14766T of MT-CYB genes were significantly higher in HAPE susceptibles. mtDNA copy number also plays a significant synergistic role in HAPE susceptibility. Our findings suggests that variants in MT-ND2 and MT-ND5 were predicted to confer decreased protein stability in HAPE susceptibles and in particular, highly conserved variants G4491A, A4944G and A14002G associated with haplogroup M33a2'3 may be the primary cause of susceptibility to HAPE in Indian male lowlanders.
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Rej PH, Deka R, Norton HL. Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India. Am J Hum Biol 2017; 29. [PMID: 28121389 DOI: 10.1002/ajhb.22955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation. METHODS We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom. RESULTS The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China. CONCLUSION Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region.
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Affiliation(s)
- Peter H Rej
- Department of Anthropology, University of Florida, Gainesville, Florida, 32611.,Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Ranjan Deka
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio, 45267
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Ohio, 45221
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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Bhatti S, Aslamkhan M, Attimonelli M, Abbas S, Aydin HH. Mitochondrial DNA variation in the Sindh population of Pakistan. AUST J FORENSIC SCI 2016. [DOI: 10.1080/00450618.2016.1144788] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shahzad Bhatti
- Department of Human Genetics and Molecular biology, University of Health Sciences Lahore, Lahore, Pakistan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Muhammad Aslamkhan
- Department of Human Genetics and Molecular biology, University of Health Sciences Lahore, Lahore, Pakistan
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Sana Abbas
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Hikmet Hakan Aydin
- Department of Medical Biochemistry, Ege University School of Medicine, Izmir, Turkey
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Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG. Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin. PLoS One 2015; 10:e0139192. [PMID: 26447794 PMCID: PMC4598113 DOI: 10.1371/journal.pone.0139192] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 09/10/2015] [Indexed: 11/18/2022] Open
Abstract
Historical discourses about the Caribbean often chronicle West African and European influence to the general neglect of indigenous people's contributions to the contemporary region. Consequently, demographic histories of Caribbean people prior to and after European contact are not well understood. Although archeological evidence suggests that the Lesser Antilles were populated in a series of northward and eastern migratory waves, many questions remain regarding the relationship of the Caribbean migrants to other indigenous people of South and Central America and changes to the demography of indigenous communities post-European contact. To explore these issues, we analyzed mitochondrial DNA and Y-chromosome diversity in 12 unrelated individuals from the First Peoples Community in Arima, Trinidad, and 43 unrelated Garifuna individuals residing in St. Vincent. In this community-sanctioned research, we detected maternal indigenous ancestry in 42% of the participants, with the remainder having haplotypes indicative of African and South Asian maternal ancestry. Analysis of Y-chromosome variation revealed paternal indigenous American ancestry indicated by the presence of haplogroup Q-M3 in 28% of the male participants from both communities, with the remainder possessing either African or European haplogroups. This finding is the first report of indigenous American paternal ancestry among indigenous populations in this region of the Caribbean. Overall, this study illustrates the role of the region's first peoples in shaping the genetic diversity seen in contemporary Caribbean populations.
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Affiliation(s)
- Jada Benn Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
| | - Miguel G. Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Missions Programs, National Geographic Society, Washington, D.C., United States of America
| | - Gabriel A. Torres
- Department of Anthropology, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Jill B. Gaieski
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Zoila E. Browne
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Marlon Stevenson
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
| | - Wendell Walters
- The Garifuna Heritage Foundation Inc., Kingston, St. Vincent and the Grenadines
- Sandy Bay Village, St. Vincent and the Grenadines
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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Ranasinghe R, Tennekoon KH, Karunanayake EH, Lembring M, Allen M. A study of genetic polymorphisms in mitochondrial DNA hypervariable regions I and II of the five major ethnic groups and Vedda population in Sri Lanka. Leg Med (Tokyo) 2015; 17:539-46. [PMID: 26065620 DOI: 10.1016/j.legalmed.2015.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 10/23/2022]
Abstract
Diversity of the hypervariable regions (HV) I and II of the mitochondrial genome was studied in maternally unrelated Sri Lankans (N=202) from six ethnic groups (i.e.: Sinhalese, Sri Lankan Tamil, Muslim, Malay, Indian Tamil and Vedda). DNA was extracted from blood and buccal swabs and HVI and HVII regions were PCR amplified and sequenced. Resulting sequences were aligned and edited between 16024-16365 and 73-340 regions and compared with revised Cambridge reference sequences (rCRS). One hundred and thirty-five unique haplotypes and 22 shared haplotypes were observed. A total of 145 polymorphic sites and 158 polymorphisms were observed. Hypervariable region I showed a higher polymorphic variation than hypervariable region II. Nucleotide diversities were quite low and similar for all ethnicities apart from a slightly higher value for Indian Tamils and a much lower value for the Vedda population compared to the other groups. When the total population was considered South Asian (Indian) haplogroups were predominant, but there were differences in the distribution of phylo-geographical haplogroups between ethnic groups. Sinhalese, Sri Lankan Tamil and Vedda populations had a considerable presence of West Eurasian haplogroups. About 2/3rd of the Vedda population comprised of macro-haplogroup N or its subclades R and U, whereas macro-haplogroup M was predominant in all other populations. The Vedda population clustered separately from other groups and Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils. Thus this study provides useful information for forensic analysis and anthropological studies of Sri Lankans.
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Affiliation(s)
- Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Kamani H Tennekoon
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Eric H Karunanayake
- Institute of Biochemistry, Molecular Biology & Biotechnology, University of Colombo, 90 Cumaratunga Munidasa Mawatha, Colombo 03, Sri Lanka.
| | - Maria Lembring
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical Centre, Box 815, 751 08 Uppsala, Sweden.
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Biomedical Centre, Box 815, 751 08 Uppsala, Sweden.
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Fregel R, Cabrera V, Larruga JM, Abu-Amero KK, González AM. Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route. PLoS One 2015; 10:e0129839. [PMID: 26053380 PMCID: PMC4460043 DOI: 10.1371/journal.pone.0129839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 05/13/2015] [Indexed: 01/17/2023] Open
Abstract
Background The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route. Methods MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges. Results The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians. Conclusions Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.
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Affiliation(s)
- Rosa Fregel
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
- * E-mail:
| | - Vicente Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Jose M. Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Khaled K. Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ana M. González
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
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Shetty SA, Marathe NP, Shouche YS. Opportunities and challenges for gut microbiome studies in the Indian population. MICROBIOME 2013; 1:24. [PMID: 24451035 PMCID: PMC3971629 DOI: 10.1186/2049-2618-1-24] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/21/2013] [Indexed: 05/06/2023]
Abstract
The gut microbiome is a complex ecosystem that affects the development, immunological responses and nutritional status of the host. Efforts are being made to unravel the complex interaction between the gut microbiome and host to have a greater understanding about its role in human health. Colonization of the gut by microbes begins at birth, but the succession and composition of the microbial community depends on a number of factors including, but not limited to, the age, diet, genetic composition, gender, geographic location, and health status of an individual. Therefore, inclusion of diverse human subjects in the study of the gut microbiome is indispensable. However, conducting such studies in India presents unique opportunities and challenges. The vast diversity in human genetic composition, dietary habits, and geographic distribution that exists in the Indian population adds to the complexity in understanding the gut microbiome. Gut microbiome-related studies from other parts of the world have reported a possible association of diseases such as obesity and diabetes with the human gut microbiome. In contrast, an in-depth assessment of risk factors associated with altered gut microbiome in such diseases in the Indian population is lacking. Studies including the Indian population may give insights into the association of the gut microbiome with various factors and diseases that may not be possible from studies on western populations. This review briefly discusses the significance of the gut microbiome on human health and the present status of gut microbiome studies in the Indian population. In addition, this review will highlight the unique opportunities and challenges for gut microbiome studies in the Indian population.
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Affiliation(s)
- Sudarshan Anand Shetty
- Microbial Culture Collection, National Center for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Nachiket Prakash Marathe
- Microbial Culture Collection, National Center for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Center for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
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Tipirisetti NR, Lakshmi RK, Govatati S, Govatati S, Vuree S, Singh L, Raghunadha Rao D, Bhanoori M, Vishnupriya S. Mitochondrial genome variations in advanced stage breast cancer: A case–control study. Mitochondrion 2013; 13:372-8. [DOI: 10.1016/j.mito.2013.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/09/2013] [Accepted: 04/19/2013] [Indexed: 12/19/2022]
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Isaacs S, Geduld-Ullah T, Benjeddou M. Reconstruction of major maternal and paternal lineages of the Cape Muslim population. Genet Mol Biol 2013; 36:167-76. [PMID: 23885197 PMCID: PMC3715281 DOI: 10.1590/s1415-47572013005000019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/12/2013] [Indexed: 11/28/2022] Open
Abstract
The earliest Cape Muslims were brought to the Cape (Cape Town - South Africa) from Africa and Asia from 1652 to 1834. They were part of an involuntary migration of slaves, political prisoners and convicts, and they contributed to the ethnic diversity of the present Cape Muslim population of South Africa. The history of the Cape Muslims has been well documented and researched however no in-depth genetic studies have been undertaken. The aim of the present study was to determine the respective African, Asian and European contributions to the mtDNA (maternal) and Y-chromosomal (paternal) gene pool of the Cape Muslim population, by analyzing DNA samples of 100 unrelated Muslim males born in the Cape Metropolitan area. A panel of six mtDNA and eight Y-chromosome SNP markers were screened using polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). Overall admixture estimates for the maternal line indicated Asian (0.4168) and African mtDNA (0.4005) as the main contributors. The admixture estimates for the paternal line, however, showed a predominance of the Asian contribution (0.7852). The findings are in accordance with historical data on the origins of the early Cape Muslims.
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Affiliation(s)
- Shafieka Isaacs
- Department of Biotechnology, University of the Western Cape, Bellville, Cape Town, South Africa
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Dutta A, Lourembam SD, Pradhan S, Baruah S. KIR diversity in three ethnic populations of Assam state, Northeast India. ACTA ACUST UNITED AC 2013; 82:48-52. [DOI: 10.1111/tan.12134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 04/11/2013] [Accepted: 04/23/2013] [Indexed: 11/28/2022]
Affiliation(s)
- A. Dutta
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. D. Lourembam
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. Pradhan
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. Baruah
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
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Govatati S, Tipirisetti NR, Perugu S, Kodati VL, Deenadayal M, Satti V, Bhanoori M, Shivaji S. Mitochondrial genome variations in advanced stage endometriosis: a study in South Indian population. PLoS One 2012; 7:e40668. [PMID: 22815783 PMCID: PMC3398934 DOI: 10.1371/journal.pone.0040668] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/11/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Endometriosis is a chronic gynecological benign disease that shares several features similar to malignancy. Mitochondrial DNA (mtDNA) mutations have been reported in all most all types of tumors. However, it is not known as to whether mtDNA mutations are associated with endometriosis. METHODOLOGY We sequenced the entire mitochondrial genome of analogous ectopic and eutopic endometrial tissues along with blood samples from 32 advanced stage endometriosis patients to analyze the role of somatic and germ-line mtDNA variations in pathogenesis of endometriosis. All ectopic tissues were screened for tumor-specific mtDNA deletions and microsatellite instability (MSI). We also performed mtDNA haplogrouping in 128 patients and 90 controls to identify its possible association with endometriosis risk. PRINCIPAL FINDINGS We identified 51 somatic (novel: 31; reported: 20) and 583 germ-line mtDNA variations (novel: 53; reported: 530) in endometriosis patients. The A13603G, a novel missense mutation which leads to a substitution from serine to glycine at the codon 423 of ND5 gene showed 100% incidence in ectopic tissues. Interestingly, eutopic endometrium and peripheral leukocytes of all the patients showed heteroplasmy (A/G; 40-80%) at this locus, while their ectopic endometrium showed homoplasmic mutant allele (G/G). Superimposition of native and mutant structures of ND5 generated by homology modeling revealed no structural differences. Tumor-specific deletions and MSI were not observed in any of the ectopic tissues. Haplogrouping analysis showed a significant association between haplogroup M5 and endometriosis risk (P: 0.00069) after bonferroni correction. CONCLUSIONS Our findings substantiate the rationale for exploring the mitochondrial genome as a biomarker for the diagnosis of endometriosis.
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Affiliation(s)
- Suresh Govatati
- Department of Biochemistry, Osmania University, Hyderabad, Andhra Pradesh, India
| | | | - Shyam Perugu
- Department of Biochemistry, Osmania University, Hyderabad, Andhra Pradesh, India
| | | | - Mamata Deenadayal
- Infertility Institute and Research Centre, Secundrabad, Andhra Pradesh, India
| | - Vishnupriya Satti
- Department of Genetics, Osmania University, Hyderabad, Andhra Pradesh, India
| | - Manjula Bhanoori
- Department of Biochemistry, Osmania University, Hyderabad, Andhra Pradesh, India
| | - S. Shivaji
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
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Salihović MP, Barešić A, Klarić IM, Cukrov S, Lauc LB, Janićijević B. The role of the Vlax Roma in shaping the European Romani maternal genetic history. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:262-70. [DOI: 10.1002/ajpa.21566] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/09/2011] [Indexed: 11/07/2022]
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Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 2010; 125:841-8. [PMID: 21184092 DOI: 10.1007/s00414-010-0540-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1'5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.
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