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Tayyeh AM, Sequeira JJ, Kumar L, Babu I, van Driem G, Mustak MS. The maternal ancestry of the Kavaratti islanders and the last glacial maximum aftermath. Mol Genet Genomics 2023; 298:1467-1477. [PMID: 37823939 DOI: 10.1007/s00438-023-02072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023]
Abstract
The prehistoric human settlement of the Lakshadweep islands remains a mystery for various reasons. Uncertainty about the existence of indigenous tribes in these islands and the lack of folklore records present major obstacles to the reconstruction of Lakshadweep ancestry. However, with extant population data, we seek to understand the maternal ancestry of the Kavaratti islanders. Mitochondrial control region variation analysis of 80 individuals from this island shows maternal links with the populations in the northwestern region of the South Asian mainland. The founder clade R30b2, observed in the Kavaratti islanders, is so far present only in the Scheduled Castes from the Punjab region, Jat Sikhs and Nairs. All other mainland populations carry basal R30 or R30a subclades. The presence of a specific Uralic U4 lineage in our samples, in addition to the Indo-European affinity observed in the phylogeny tree, substantiates a northwestern maternal ancestry of the Kavaratti islanders and implies an ancestral admixture with early humans in the Near East at the time of the last glacial maximum (LGM). Based on our Bayesian analysis, we furthermore propose that a group bearing mostly R30b2 during the LGM recovery, moved eastward and southward, where they received Indian-specific M haplogroups. Hence, the maternal ancestry of the Kavaratti islanders is evidently a consequence of the demographic changes in the northwestern region of the Indian subcontinent caused by the Last Glacial Maximum. The haplogroup distribution pattern and nucleotide sequence data produced in this study will enrich the forensic database of the Lakshadweep islands.
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Affiliation(s)
- Alnoman Mundher Tayyeh
- Department of Applied Zoology, Mangalore University, Mangalagangothri, 574199, India
- Department of Biosciences, Biotechnology Unit, Mangalore University, Mangalagangothri, 574199, India
| | | | - Lomous Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Idrees Babu
- Department of Science and Technology, Lakshadweep Administration, Kavaratti, 682555, India
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012, Bern, Switzerland
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Singh PP, Kumar S, Pasupuleti N, Weerasooriya P, van Driem G, Tennekoon KH, Rai N, Chaubey G, Ranasinghe R. Reconstructing the population history of the Sinhalese, the major ethnic group in Śrī Laṅkā. iScience 2023; 26:107797. [PMID: 37744037 PMCID: PMC10514440 DOI: 10.1016/j.isci.2023.107797] [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: 07/06/2023] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
The Sinhalese are the major ethnic group in Śrī Laṅkā, inhabiting nearly the whole length and breadth of the island. They speak an Indo-European language of the Indo-Iranian branch, which is held to originate in northwestern India, going back to at least the fifth century BC. Previous genetic studies on low-resolution markers failed to infer the genomic history of the Sinhalese population. Therefore, we have performed a high-resolution fine-grained genetic study of the Sinhalese population and, in the broader context, we attempted to reconstruct the genetic history of Śrī Laṅkā. Our allele-frequency-based analysis showed a tight cluster of Sinhalese and Tamil populations, suggesting strong gene flow beyond the boundary of ethnicity and language. Interestingly, the haplotype-based analysis preserved a trace of the North Indian affiliation to the Sinhalese population. Overall, in the South Asian context, Śrī Laṅkān ethnic groups are genetically more homogeneous than others.
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Affiliation(s)
- Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - Sachin Kumar
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226607, India
| | | | - P.R. Weerasooriya
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03 00300, Śrī Laṅkā
| | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Länggassstrasse 49, 3012 Bern, Switzerland
| | - Kamani H. Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03 00300, Śrī Laṅkā
| | - Niraj Rai
- Ancient DNA Lab, Birbal Sahni Institute of Palaeosciences, Lucknow 226607, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India
| | - R. Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, No. 90, Cumaratunga Munidasa Mawatha, Colombo 03 00300, Śrī Laṅkā
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Sooriyabandara MGC, Bandaranayake AU, Hathurusinghe HABM, Jayasundara SM, Marasinghe MSRRP, Prasad GAT, Abeywardana VPMK, Pinidiya MA, Nilanthi RMR, Bandaranayake PCG. A unique single nucleotide polymorphism in Agouti Signalling Protein (ASIP) gene changes coat colour of Sri Lankan leopard (Panthera pardus kotiya) to dark black. PLoS One 2023; 18:e0269967. [PMID: 37440497 PMCID: PMC10343082 DOI: 10.1371/journal.pone.0269967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
The Sri Lankan leopard (Panthera pardus kotiya) is an endangered subspecies restricted to isolated and fragmented populations in Sri Lanka. Among them, melanistic leopards have been recorded on a few occasions. Literature suggests the evolution of melanism several times in the Felidae family, with three species having distinct mutations. Nevertheless, the mutations or other variations in the remaining species, including Sri Lankan melanistic leopard, are unknown. We used reference-based assembled nuclear genomes of Sri Lankan wild type and melanistic leopards and de novo assembled mitogenomes of the same to investigate the genetic basis, adaptive significance, and evolutionary history of the Sri Lankan melanistic leopard. Interestingly, we identified a single nucleotide polymorphism in exon-4 Sri Lankan melanistic leopard, which may completely ablate Agouti Signalling Protein (ASIP) function. The wild type leopards in Sri Lanka did not carry this mutation, suggesting the cause for the occurrence of melanistic leopords in the population. Comparative analysis of existing genomic data in the literature suggests it as a P. p. kotiya specific mutation and a novel mutation in the ASIP-gene of the Felidae family, contributing to naturally occurring colour polymorphism. Our data suggested the coalescence time of Sri Lankan leopards at ~0.5 million years, sisters to the Panthera pardus lineage. The genetic diversity was low in Sri Lankan leopards. Further, the P. p. kotiya melanistic leopard is a different morphotype of the P. p. kotiya wildtype leopard resulting from the mutation in the ASIP-gene. The ability of black leopards to camouflage, along with the likelihood of recurrence and transfer to future generations, suggests that this rare mutation could be environment-adaptable.
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Affiliation(s)
| | - A. U. Bandaranayake
- Department of Computer Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - H. A. B. M. Hathurusinghe
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. M. Jayasundara
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - G. A. T. Prasad
- Department of Wildlife Conservation, Battaramulla, Sri Lanka
| | | | - M. A. Pinidiya
- Department of Wildlife Conservation, Battaramulla, Sri Lanka
| | | | - P. C. G. Bandaranayake
- Agricultural Biotechnology Centre, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
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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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Wijekoon N, Gonawala L, Ratnayake P, Sirisena D, Gunasekara H, Dissanayake A, Senanayake S, Keshavaraj A, Hathout Y, Steinbusch HW, Mohan C, Dalal A, Hoffman E, D de Silva K. Gene therapy for selected neuromuscular and trinucleotide repeat disorders - An insight to subsume South Asia for multicenter clinical trials. IBRO Neurosci Rep 2023; 14:146-153. [PMID: 36819775 PMCID: PMC9931913 DOI: 10.1016/j.ibneur.2023.01.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Background In this article, the authors discuss how they utilized the genetic mutation data in Sri Lankan Duchenne muscular dystrophy (DMD), Spinal muscular atrophy (SMA), Spinocerebellar ataxia (SCA) and Huntington's disease (HD) patients and compare the available literature from South Asian countries to identifying potential candidates for available gene therapy for DMD, SMA, SCA and HD patients. Methods Rare disease patients (n = 623) with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy were genetically confirmed using Multiplex Ligation Dependent Probe Amplification (MLPA), and single plex PCR. A survey was conducted in the "Wiley database on Gene Therapy Trials Worldwide" to identify DMD, SMA, SCA, and HD gene therapy clinical trials performed worldwide up to April 2021. In order to identify candidates for gene therapy in other neighboring countries we compared our findings with available literature from India and Pakistan which has utilized the same molecular diagnostic protocol to our study. Results From the overall cohort of 623 rare disease patients with the characteristic clinical findings suspected of HD, SCA, SMA and Muscular Dystrophy, n = 343 (55%) [Muscular Dystrophy- 65%; (DMD-139, Becker Muscular Dystrophy -BMD-11), SCA type 1-3-53% (SCA1-61,SCA2- 23, SCA3- 39), HD- 52% (45) and SMA- 34% (22)] patients were positive for molecular diagnostics by MLPA and single plex PCR. A total of 147 patients in Sri Lanka amenable to available gene therapy; [DMD-83, SMA-15 and HD-49] were identified. A comparison of Sri Lankan finding with available literature from India and Pakistan identified a total of 1257 patients [DMD-1076, SMA- 57, and HD-124] from these three South Asian Countries as amenable for existing gene therapy trials. DMD, SMA, and HD gene therapy clinical trials (113 studies) performed worldwide up to April 2021 were concentrated mostly (99%) in High Income Countries (HIC) and Upper Middle-Income Countries (UMIC). However, studies on the potential use of anti-sense oligonucleotides (ASO) for treatment of SCAs have yet to reach clinical trials. Conclusion Most genetic therapies for neurodegenerative and neuromuscular disorders have been evaluated for efficacy primarily in Western populations. No multicenter gene therapy clinical trial sites for DMD, SMA and HD in the South Asian region, leading to lack of knowledge on the safety and efficacy of such personalized therapies in other populations, including South Asians. By fostering collaboration between researchers, clinicians, patient advocacy groups, government and industry in gene therapy initiatives for the inherited-diseases community in the developing world would link the Global North and Global South and breathe life into the motto "Together we can make a difference".
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Key Words
- BMD, Becker muscular dystrophy
- Bio Bank
- DMD, Duchenne muscular dystrophy
- Developing Countries
- Duchenne Muscular Dystrophy
- EMA, European Medical Agency
- EMQN, European Molecular Quality Genetics Network
- FDA, U. S. Food and Drug Administration
- HD, Huntington’s disease
- HIC, High Income Countries
- Huntington’s Disease
- Indian Sub-continent
- MLPA, Multiplex Ligation Dependent Probe Amplification
- Neurogenetic Disorders
- SCA, Spinocerebellar ataxia
- SMA, Spinal muscular atrophy
- Spinal Muscular Atrophy
- Spinocerebellar Ataxia
- UMIC, Upper Middle Income Countries
- WTO, World Trade Organization
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Affiliation(s)
- Nalaka Wijekoon
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | - Lakmal Gonawala
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands
| | | | | | | | | | | | | | - Yetrib Hathout
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - Harry W.M. Steinbusch
- School for Mental Health and Neuroscience, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, the Netherlands,EURON - European Graduate School of Neuroscience, the Netherlands,Dept. of Brain & Cognitive Sciences, Daegu Gyeungbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Chandra Mohan
- Department of Bioengineering, University of Houston, Houston, TX, USA
| | - Ashwin Dalal
- Diagnostics Division, Center for DNA Fingerprinting and Diagnostics, India
| | - Eric Hoffman
- Pharmaceutical Sciences Department, School of Pharmacy and Pharmaceutical Sciences, Binghamton University, New York, USA
| | - K.Ranil D de Silva
- Interdisciplinary Centre for Innovations in Biotechnology and Neuroscience, University of Sri Jayewardenepura, Nugegoda, Sri Lanka,EURON - European Graduate School of Neuroscience, the Netherlands,Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka,Corresponding author at: Institute for Combinatorial Advanced Research and Education (KDU-CARE), General Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.
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Mitochondrial DNA (CA) n dinucleotide repeat variations in Sinhalese and Vedda populations in Sri Lanka. Genetica 2022; 150:145-150. [PMID: 35141800 DOI: 10.1007/s10709-022-00150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 01/27/2022] [Indexed: 11/04/2022]
Abstract
Sinhalese and Vedda people are respectively the major ethnic group and the descendants of the probably earliest inhabitants of Sri Lanka, both believed to have a long history of settlement on the island. However, very little information is available on the origin and possible migration patterns of the two populations. Some studies have focused on (CA) dinucleotide repeat variations located in the mitochondrial hypervariable region 3 (HVS3) (base pairs 514-524) as a useful biomarker to understand migration patterns of different populations. Hence, here we analyze these repeat variations in these two ethnic groups to understand their historical roots and possible patterns of gene flow. Blood samples were collected from healthy, maternally unrelated individuals (N = 109) and mitochondrial D-loop was amplified and sequenced. The (CA)4 dinucleotide repeat in hypervariable region 3 was detected in the majority of Vedda samples while the remaining samples were defined by a (CA)5 cluster. In contrast, the (CA)5 repeat was the most frequent among Sinhalese followed by (CA)4 and (CA)7 repeats. Haplogroup diversity of (CA)4 variation indicated that the majority of Sinhalese individuals grouped into the M30 haplogroup while Vedda clustered into the R5a2b and U7a2 haplogroups. No significant differences in diversity measures were observed among the two populations. However, Multidimensional Scaling indicated a separate clustering for aboriginal Vedda and contemporary Sinhalese populations. Results from this study can be used together with mitochondrial DNA information from hypervariable regions 1 and 2 to perform anthropological and forensic investigations in the two populations studied.
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Perera N, Galhena G, Ranawaka G. X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations. Sci Rep 2021; 11:12748. [PMID: 34140598 PMCID: PMC8211843 DOI: 10.1038/s41598-021-92314-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
A new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.
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Affiliation(s)
- Nandika Perera
- Genetech Molecular Diagnostics, Colombo 08, Sri Lanka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
| | - Gayani Galhena
- Department of Zoology and Environment Sciences, University of Colombo, Colombo 03, Sri Lanka.
| | - Gaya Ranawaka
- Faculty of Health Sciences, The Open University of Sri Lanka, Nawala, Sri Lanka
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Seshasubramanian V, SathishKannan AD, Naganathan C, Narayan S, Periathiruvadi S. Molecular analysis of HLA Class I and Class II genes in five different South Indian linguistic groups. HLA 2021; 97:399-419. [PMID: 33583139 DOI: 10.1111/tan.14219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 01/16/2021] [Accepted: 02/08/2021] [Indexed: 11/30/2022]
Abstract
South Indians are a heterogeneous population who speak different languages and differ in their life style and physical appearance. Major population movements, social structure and caste endogamy have influenced the genetic structure of Indian populations. The human leukocyte antigen (HLA) system of populations is highly informative because of the high level of polymorphisms. Knowledge of allele and haplotype frequencies of the HLA system is important in the search for unrelated bone marrow donors. We investigated the distribution of HLA A, B, C, DRB1 and DQB1 loci in five linguistic groups from South India. HLA-A*01:01:01~B*57:01:01:01~C*06:02:01~DRB1*07:01:01~DQB1*03:03:02 was the common haplotype with highest frequency in all the five populations studied. A few relevant haplotypes were identified as most common haplotypes in each linguistic group. Comparison of HLA-A, -B and -DRB1 allele distribution in these five linguistic groups with the other Asian population showed that the South Indian populations were closely related to Sri Lankan populations. A large South Indian donor registry might serve as good source of donors for patients from Sri Lanka and vice versa.
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Affiliation(s)
| | | | | | - Saranya Narayan
- JEENOMICS (NGS HLA laboratory), Jeevan Stem Cell Foundation, Chennai, India
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Tiphania Kotelawala J, Ranasinghe R, Rodrigo C, Tennekoon KH, Silva KD. Evaluation of non-coding region sequence variants and mitochondrial haplogroups as potential biomarkers of sporadic breast cancer in individuals of Sri Lankan Sinhalese ethnicity. Biomed Rep 2020; 12:339-347. [PMID: 32346478 DOI: 10.3892/br.2020.1292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations have been reported to be associated with various diseases, including cancer. The present study investigated the mtDNA non-coding region mutations and mitochondrial haplogroups as potential biomarkers of sporadic breast cancer in Sri Lankan Sinhalese women. Mitochondrial macro-haplogroups were determined using PCR-restriction fragment length polymorphism, whereas non-coding region sequences were determined using Sanger sequencing. The sequence of the non-coding region was also used to confirm haplogroup status. Neither the mutations in the non-coding region nor the mitochondrial haplogroups that were reported as risk factors in other populations, were determined to be potential risk factors for sporadic breast cancer in the present study. Furthermore, several novel mutations were identified in the present matched pairs case-controlled study. The M65a haplogroup with an additional mutation at position 16311 (P=0.0771) and mutations at the ori-b site (P=0.05) were considered a weak risk factor and protective factor, respectively, for sporadic breast cancer in Sinhalese women. Previous studies have indicated the use of mtDNA mutations as a biomarker; however, the present study showed that such biomarkers need to be validated for individual ethnic groups before they can be recommended for use in the prediction of disease.
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Affiliation(s)
- Joanne Tiphania Kotelawala
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka
| | - Ruwandi Ranasinghe
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka
| | - Chrishani Rodrigo
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka
| | - Kamani Hemamala Tennekoon
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo 00300, Sri Lanka
| | - Kanishka De Silva
- National Cancer Institute, Apeksha Hospital, Maharagama 10280, Sri Lanka
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KULATILAKE SAMANTI. The Sarasins’ Collection of Historical Sri Lankan Crania. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- SAMANTI KULATILAKE
- Department of Sociology and Anthropology, Mount Royal University, Calgary
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Sooriyakanthan M, Wimalasekera S, Kanagasabai S. Establishment of Reference Norms for Lung Function Parameters of Healthy Sri Lankan Tamils. Pulm Med 2019; 2019:2169627. [PMID: 31934448 PMCID: PMC6942901 DOI: 10.1155/2019/2169627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/11/2019] [Accepted: 11/21/2019] [Indexed: 11/17/2022] Open
Abstract
Spirometry and Peak Expiratory Flow Rate (PEFR) are important measurements in diagnosing and monitoring of COPD and asthma. Ethnic specific reference equations are necessary in interpretation of these parameters. However, equations for Sri Lankan Tamil adults are not available. This study aims to establish reference equations for lung function parameters of Sri Lankan Tamils. A descriptive cross sectional study was carried out in all 5 districts of Northern Sri Lanka. Participants were selected by cluster sampling. Base line data were obtained by a questionnaire. Height, sitting height, weight, arm span, mid arm circumference, and chest expansion were measured. Respiratory functions were assessed by a calibrated spirometer (Cosmed Micro Quark, Italy) and Wright compatible peak expiratory flow meter. Means, and standard deviations for Vital Capacity (VC), Forced Vital Capacity (FVC), Forced Expiratory Volume in the first second (FEV1), FEV1%, Peak Expiratory Flow Rate (PEFR) and for other forced expiratory parameters of 775 males and 687 females were determined. Lung function parameters have significant (p < 0.05) positive correlations with most of the anthropometric measures. Age had a significant (p < 0.05) negative correlation with lung function parameters in adults >20 years and positive correlation (p < 0.05) in 14-20 years group. Step wise multiple regression analysis was used to determine the prediction equations. Also equations based on age, height and age, arm span were derived. Age, height based equations were retested in the same population. Predicted values by the developed equations had better agreement than that of GLI 2012 equations. This can be useful in assessing the respiratory function in Sri Lankan Tamil population as there are no already existing equations.
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Affiliation(s)
| | - Savithri Wimalasekera
- Department Physiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Sivapalan Kanagasabai
- Department of Physiology, Faculty of Medicine, University of Jaffna, Jaffna, Sri Lanka
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Indika NLR, Vidanapathirana DM, Dilanthi HW, Kularatnam GAM, Chandrasiri NDPD, Jasinge E. Phenotypic spectrum and genetic heterogeneity of cystic fibrosis in Sri Lanka. BMC MEDICAL GENETICS 2019; 20:89. [PMID: 31126253 PMCID: PMC6534844 DOI: 10.1186/s12881-019-0815-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 04/24/2019] [Indexed: 11/13/2022]
Abstract
Background Cystic fibrosis has been largely under-diagnosed and thus, limited data is available on the incidence of cystic fibrosis in Sri Lanka. Our aim is to describe the phenotypic and genotypic spectrum of children with cystic fibrosis in Sri Lanka. Case presentation This report describes 10 unrelated cystic fibrosis cases with phenotypic features of cystic fibrosis and abnormal or intermediate sweat tests. The most common phenotypic features in this sample of symptomatic patients were persistent or recurrent lower respiratory tract infections, failure to thrive and Pseudo-Bartter syndrome. Altogether 7 cystic fibrosis causing mutations were identified in 10 patients. Except delta F508 which is the commonest mutation worldwide all the other mutations detected in Sri Lankan patients are rare mutations. 1161delC and V456A detected in our patients are South Asian mutations. The other mutations such as [C.1282C > G; C.2738A > G], C.53 + 1G > C, 2184insA and a deletion encompassing exons 4 to 11 have been reported previously from European patients with cystic fibrosis. Conclusion These cases highlight the importance of considering the diagnosis of cystic fibrosis in children and young adults presenting with persistent respiratory tract infections associated with severe malnutrition and Pseudo-Bartter syndrome, especially in low income countries where newborn screening for cystic fibrosis is not available. The spectrum of CFTR mutations in Sri Lanka is heterogeneous and possibly linked to genetic flow from Indian subcontinent and Europe. The common mutations should be identified by sequencing the entire CFTR gene in adequate number of cystic fibrosis patients in order to design a mutation panel for common regional mutations.
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Affiliation(s)
- Neluwa Liyanage Ruwan Indika
- Department of Biochemistry, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.
| | | | - Hewa Warawitage Dilanthi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | | | | | - Eresha Jasinge
- Department of Chemical Pathology, Lady Ridgeway Hospital for Children, Colombo 8, Sri Lanka
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14
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Mustak MS, Rai N, Naveen MR, Prakash S, Carlus SJ, Pasupuleti N, Srivastava A, Singh PP, Babu I, Dubey PK, Chaubey G, Thangaraj K. The peopling of Lakshadweep Archipelago. Sci Rep 2019; 9:6968. [PMID: 31061397 PMCID: PMC6502849 DOI: 10.1038/s41598-019-43384-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 04/23/2019] [Indexed: 11/09/2022] Open
Abstract
The archipelago of Lakshadweep is considered as a stopover to the maritime route since ancient time. It is not very clear when the human first occupied these islands, however in the long history of the islands, the local legends suggest that Lakshadweep has been ruled by different kingdoms. To have a better understanding of peopling of Lakshadweep, we have analysed 557 individuals from eight major islands for mitochondrial DNA and 166 individuals for Y chromosome markers. We found a strong founder effect for both paternal and maternal lineages. Moreover, we report a close genetic link of Lakshadweep islanders with the Maldives, Sri Lanka and India. Most of the Lakshadweep islands share the haplogroups specific to South Asia and West Eurasia, except Minicoy Island that also shares haplogroups of East Eurasia. The paternal and maternal ancestries of the majority of island populations suggest their arrival from distinct sources. We found that the maternal ancestry was closer to South Indian populations, whereas the paternal ancestry was overwhelmed with the haplogroups, more common in the Maldives and North of India. In conclusion, our first genetic data suggest that the majority of human ancestry in Lakshadweep is largely derived from South Asia with minor influences from East and West Eurasia.
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Affiliation(s)
- Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalore, 574199, India.,CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, 53 University Road, Lucknow, 226007, India
| | - Mohan Rao Naveen
- Department of Applied Zoology, Mangalore University, Mangalore, 574199, India
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - S Justin Carlus
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | | | - Anshika Srivastava
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Prajjval Pratap Singh
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Idrees Babu
- Department of Science and Technology, Lakshadweep Administration, Kavaratti, 682555, India
| | - Pavan Kumar Dubey
- Prosthodontics Unit, Faculty of Dental Sciences, Institute of Medical Sciences, Varanasi, 221005, India
| | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, 5100, Estonia
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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15
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Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India. Genetica 2018; 146:383-389. [PMID: 30032461 DOI: 10.1007/s10709-018-0030-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 07/15/2018] [Indexed: 11/28/2022]
Abstract
The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.
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Affiliation(s)
- Charles Sylvester
- Department of Studies in Zoology, University of Mysore, Mysore, India.,Anthropological Survey of India, Southern Regional Center, Mysore, India
| | | | - Jaya Sankar Rao
- Anthropological Survey of India, Southern Regional Center, Mysore, India
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16
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Roberts P, Gillingwater TH, Lahr MM, Lee-Thorp J, MacCallum M, Petraglia M, Wedage O, Heenbanda U, Wainnya-laeto U. Historical Tropical Forest Reliance amongst the Wanniyalaeto (Vedda) of Sri Lanka: an Isotopic Perspective. HUMAN ECOLOGY: AN INTERDISCIPLINARY JOURNAL 2018; 46:435-444. [PMID: 29997411 PMCID: PMC6015624 DOI: 10.1007/s10745-018-9997-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Headland and Bailey (1991) argued in Human Ecology that tropical forests could not support long-term human foraging in the absence of agriculture. Part of their thesis was based on the fact that supposedly isolated 'forest' foragers, such as the Wanniyalaeto (or Vedda) peoples of Sri Lanka, could be demonstrated to be enmeshed within historical trade networks and rely on crops as part of their overall subsistence. Yet, in the same volume and in the years that followed scholars have presented ethnographic and archaeological evidence, including from Sri Lanka, that counter this proposition, demonstrating the occupation and exploitation of tropical rainforest environments back to 38,000 years ago (ka) in this part of the world. However, archaeological and ethnohistorical research has yet to quantify the overall reliance of human foragers on tropical forest resources through time. Here, we report stable carbon and oxygen isotope data from historical Wanniyalaeto individuals from Sri Lanka, in full collaboration with the present-day members of this group, that suggest that while a number of individuals made use of agricultural resources in the recent past, others subsisted primarily on tropical forest resources as late as the 1800s.
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Affiliation(s)
- Patrick Roberts
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK
| | - Thomas H. Gillingwater
- Anatomical Museum, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Marta Mirazon Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, UK
| | - Julia Lee-Thorp
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, University of Oxford, Oxford, UK
| | - Malcolm MacCallum
- Anatomical Museum, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | - Oshan Wedage
- Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
- Department of History and Archaeolpogy, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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17
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Genetic diversity of variants involved in drug response and metabolism in Sri Lankan populations: implications for clinical implementation of pharmacogenomics. Pharmacogenet Genomics 2016; 26:28-39. [PMID: 26444257 PMCID: PMC4890825 DOI: 10.1097/fpc.0000000000000182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Supplemental Digital Content is available in the text. Background Interpopulation differences in drug responses are well documented, and in some cases they correspond to differences in the frequency of associated genetic markers. Understanding the diversity of genetic markers associated with drug response across different global populations is essential to infer population rates of drug response or risk for adverse drug reactions, and to guide implementation of pharmacogenomic testing. Sri Lanka is a culturally and linguistically diverse nation, but little is known about the population genetics of the major Sri Lankan ethnic groups. The objective of this study was to investigate the diversity of pharmacogenomic variants in the major Sri Lankan ethnic groups. Methods We examined the allelic diversity of more than 7000 variants in genes involved in drug biotransformation and response in the three major ethnic populations of Sri Lanka (Sinhalese, Sri Lankan Tamils, and Moors), and compared them with other South Asian, South East Asian, and European populations using Wright’s Fixation Index, principal component analysis, and STRUCTURE analysis. Results We observed overall high levels of similarity within the Sri Lankan populations (median FST=0.0034), and between Sri Lankan and other South Asian populations (median FST=0.0064). Notably, we observed substantial differentiation between Sri Lankan and European populations for important pharmacogenomic variants related to warfarin (VKORC1 rs9923231) and clopidogrel (CYP2C19 rs4986893) response. Conclusion These data expand our understanding of the population structure of Sri Lanka, provide a resource for pharmacogenomic research, and have implications for the clinical use of genetic testing of pharmacogenomic variants in these populations.
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18
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Kimel SY, Huesmann R, Kunst JR, Halperin E. Living in a Genetic World. PERSONALITY AND SOCIAL PSYCHOLOGY BULLETIN 2016; 42:688-700. [DOI: 10.1177/0146167216642196] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 02/28/2016] [Indexed: 11/16/2022]
Abstract
Information about the degree of one’s genetic overlap with ethnic outgroups has been emphasized in genocides, is frequently learned about through media reporting, and is increasingly being accessed via personal genetic testing services. However, the consequence of learning about whether your own ethnic group is either genetically related to or genetically distinct from a disliked ethnic group remains unknown. Across four experiments, using diverse samples, measures and contexts, we demonstrate that altering perceptions of genetic overlap between groups in conflict—in this case Arabs and Jews—impacts factors that are directly related to interethnic hostility (e.g., aggressive behaviors, support of conflict-related policies). Our findings indicate that learning about the genetic difference between oneself and an ethnic outgroup may contribute to the promotion of violence, whereas learning about the similarities may be a vital step toward fostering peace in some contexts. Possible interventions and implications are discussed.
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Affiliation(s)
| | | | - Jonas R. Kunst
- Harvard University, Cambridge, MA, USA
- University of Oslo, Norway
- University of Aarhus, Denmark
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19
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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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20
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Palanichamy MG, Mitra B, Zhang CL, Debnath M, Li GM, Wang HW, Agrawal S, Chaudhuri TK, Zhang YP. West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system. Hum Genet 2015; 134:637-47. [PMID: 25832481 DOI: 10.1007/s00439-015-1547-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 11/28/2022]
Abstract
There is no indication from the previous mtDNA studies that west Eurasian-specific subclades have evolved within India and played a role in the spread of languages and the origins of the caste system. To address these issues, we have screened 14,198 individuals (4208 from this study) and analyzed 112 mitogenomes (41 new sequences) to trace west Eurasian maternal ancestry. This has led to the identification of two autochthonous subhaplogroups--HV14a1 and U1a1a4, which are likely to have originated in the Dravidian-speaking populations approximately 10.5-17.9 thousand years ago (kya). The carriers of these maternal lineages might have settled in South India during the time of the spread of the Dravidian language. In addition to this, we have identified several subsets of autochthonous U7 lineages, including U7a1, U7a2b, U7a3, U7a6, U7a7, and U7c, which seem to have originated particularly in the higher-ranked caste populations in relatively recent times (2.6-8.0 kya with an average of 5.7 kya). These lineages have provided crucial clues to the differentiation of the caste system that has occurred during the recent past and possibly, this might have been influenced by the Indo-Aryan migration. The remaining west Eurasian lineages observed in the higher-ranked caste groups, like the Brahmins, were found to cluster with populations who possibly arrived from west Asia during more recent times.
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Affiliation(s)
- Malliya Gounder Palanichamy
- Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, 650 091, Yunnan, China,
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Language isolates and their genetic identity: a commentary on mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations. J Hum Genet 2013; 59:61-3. [PMID: 24257474 DOI: 10.1038/jhg.2013.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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