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Unrooted neighbor-joining (NJ) tree of the 21 Sri Lankan populations based on the net genetic distances. (Abbreviations are given in Supplementary Table S1).
Source publication
Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among...
Contexts in source publication
Context 1
... unrooted neighbor-joining tree was constructed for phylo- genetic relationships among 21 subgroups of five ethnic populations of Sri Lanka as illustrated in Figure 2. Another phylogenetic construction was also performed for the five ethnic populations when all subgroups within a population were collapsed; the result is shown in Supplementary Figure S1. ...
Context 2
... Sinhalese formed close genetic affiliations with Sri Lankan Tamils and Low-country Sinhalese. Figure 2 illustrates more insights into the genetic relationships among the studied populations, with the description of genetic variation among subgroups within each ethnic population. From this unrooted neighbor-joining tree, it was confirmed that there was a greater genetic distance between the Vedda people and the rest of the populations. ...
Context 3
... speaking, Vedda mtDNA variation in Sri Lanka L Ranaweera et al subgroups were more dispersed on the PCA map than within any other ethnic population, reflecting greater diversity among them. PCA map constructed from the net genetic distances from HVS-1 and part of HVS-2 sequences, which is in agreement with the PCA map constructed from haplogroup distribution frequencies, is also shown in Supplementary Figure S2. The PCA is extended further to include various other ethnic populations from the Indian subcontinent (Supplementary Table S2) Figure 4. ...
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Citations
... Intriguingly, it has been documented that approximately 85,000 years ago, the first wave of human migration out of Africa followed the coast through the Middle East into Southern Asia via Sri Lanka (Kundu and Ghosh, 2015). Most importantly, the only precursor of modern human fossils in South Asia, dating back 37,000 years, was found in Sri Lanka (Ranaweera et al., 2014). ...
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... The few mitochondrial DNA studies from Sri Lanka show that the Vedda do not cluster closely with either European or North Asian groups (Harihara et al., 1988). The first high resolution noncoding region mitochondrial DNA study of the Sri Lanka population revealed the reduced intrapopulation genetic diversity among subgroups of the Vedda people (Ranaweera et al., 2014a). Another such study reveals that the Vedda population clustered separately from other groups and that Sri Lankan Tamils showed a closer genetic affiliation to Sinhalese than to Indian Tamils (Ranasinghe et al., 2021). ...
... Moreover, the last two studies showed that most Vedda exhibit West Eurasian lineages alongside Indian ancestries. Another study suggests that the Vedda population is a genetically drifted group with limited gene flow from neighboring Sinhalese and Sri Lankan Tamil populations (Ranaweera et al., 2014a;Ranasinghe et al., 2021). ...
... The importance of Sri Lanka's geographic location is further emphasized by several anthropological studies, including De Silva's suggestion that Vedda groups represent a mixture of Australoid, African, and Mediterranean affinities (De Silva, 1981). Interestingly, previous genetic research revealed that the Village Vedda possess West Eurasian genetic ancestry (Ranaweera et al., 2014a) and provided genetic evidence of early modern human dispersal (Ranaweera et al., 2014b). Therefore, the presence of broader noses in the Coastal Indigenous people, comparable to that of African populations, and presence of very long face/long face which is similar to Malaysian population might indicate presence of ancient genetic footprints. ...
The existence of an indigenous community within a country is a source of pride and warrants significant attention. Sri Lanka is no exception, and, as a country with the fossil remains of anatomically modern Homo sapiens, it is hypothesized that Sri Lankan Indigenous people might harbor ancient genetic signatures. This study aims to establish baseline data of certain craniofacial anthropometric measurements in the Coastal Indigenous people and classify their head, face, and nose types. This study involved 126 (70 Male and 56 Female) unrelated individuals from six villages, representing the Coastal Indigenous population. Sixteen craniofacial measurements were obtained, providing calculations of three craniofacial indices: the Cephalic index, Facial index, and Nasal index. It was apparent that all craniofacial measurements, except nose protrusion of males, had significantly higher dimensions than those of the female participants. In addition to baseline quantitative raw data, the calculated indices are as follows: The mean cephalic, facial, and nasal indices of females were 78.50± 4.84, 88.37±13.06, and 93.93±12.23, respectively, whereas those of males were 78.85±5.76, 91.74±13.70, and 94.58±14.06, respectively. This is the first craniofacial study on Coastal Indigenous people in Sri Lanka. The most common head shape observed among both genders was mesocephalic. Males predominantly exhibited a hyperleptoprosopic facial type, while females mostly showed a leptoprosopic facial type. The most dominant nasal type recorded for both genders was the platyrrhine nasal phenotype. Interestingly, such platyrrhine nose is rarely present in other world populations, except in African populations.
... Owing to the increasing significance of Sri Lanka in the discourse on human evolution, there has been a continued proliferation of publications focusing on genetic diversity (Ellepola and Wikramanayake, 1986;Ellepola, 1990;Fernando et al., 2023;Ranasinghe et al., 2015;Ranaweera et al., 2014;Welikala et al., 2024) and Stable Isotope Analysis (Roberts et al., 2018) of Vadda populations in various parts of the island. ...
... Kennedy (1965:202) suggests that both the island's Mesolithic population and the Vaddas appear to share a common gene pool, pointing to a strong genetic affinity between them based on the high frequency of shared morphological traits. Genetic analyses conducted by Ellepola (1990) and Ranaweera et al. (2014) have revealed significant genetic similarities between the Vaddas and Sinhalese populations (also pointed out by Deraniyagala 1963e), while also indicating distinct genetic origins for the Vaddas, potentially linked to populations of the Indian subcontinent. According to Ranasinghe et al. (2015), the Vaddas also have more genetic similarity to Sinhala people than Tamil people. ...
... The fact that the Vadda population is genetically distinct from mainly Sinhalese and Tamils (Ranaweera et al., 2014), followed by the lowest genetic diversity among the six other ethnic groups of the island (Ranasinghe et al., 2015), may indicate a genetic drift with longer periods of isolation in this group. The Vadda population's gathering independently from other contemporary ethnic groups of the island (Ranasinghe et al., 2015;Ranaweera et al., 2014) may be a gauge of aiding the historical belief that they are descendants of early inhabitants who once occupied the island. ...
This paper aims to re-examine key scholarly works pertaining to the Sri Lankan Vadda, an indigenous community of the island, in order to explore extant research of the said community. Despite considerable progress, lingering misunderstandings and uncertainties persist regarding their origins, connections to prehistoric populations, affiliations with contemporary ethnic groups, and the interrelationships among different Vadda communities across the island. Furthermore, uncertainties persist regarding the authenticity of Vadda skeletal remains and the adequacy of archaeological samples, which often suffer from fragmentation and incompleteness. It is this archaeological sample that has been used to draw conclusions about the cultural and biological continuity of the Mesolithic population or the Balangoda man (Homo sapiens balangodensis) with the Vaddas and the modern populations of the island, thus perhaps distorting interpretations. Similarly, this study underscores concerns regarding the representation of modern samples collected from diverse Vadda clans inhabiting various ecological zones and engaging in different subsistence practices, potentially skewing the conclusions of preceding research. In this study, fresh ethnoarchaeological data are used to examine some misconceptions prevailing about the Warugas (clans) as well as the use of the term Wanniyalaetto as a synonym for Vaddas. Given the rapid acculturation of Vaddas, there is a pressing need for continued interdisciplinary investigations into the Vadda communities, encompassing different Warugas and geographic regions, to ensure a better understanding of their socio-cultural dynamics with the aim of enhanced insight into their evolutionary pathways.
... Numerous studies have delved into the socio-anthropological features of the Vedda population (de Silva, 2011;Parker, 1909). Research has been undertaken to gain insight into their molecular level components (Perera et al., 2021;Ranasinghe et al., 2015;Roychoudhury, 2008;Ranaweera et al. 2014). These studies have unveiled that the Vedda share genetic components with Sinhalese and Sri Lankan Tamils, whilst they also exhibit geographical affinities to tribal populations such as the Irula, Kota and Mulla Kuruma in southern India, the Semai and Senoi of the Malay peninsula and tribes of Upper Burma. ...
... These studies have unveiled that the Vedda share genetic components with Sinhalese and Sri Lankan Tamils, whilst they also exhibit geographical affinities to tribal populations such as the Irula, Kota and Mulla Kuruma in southern India, the Semai and Senoi of the Malay peninsula and tribes of Upper Burma. Two prior studies on mitochondrial Hypervariable Segment (HVS-I and HVS-II) data show that most Vedda exhibits West Eurasian lineages alongside Indian ancestries (Ranasinghe et al., 2015;Ranaweera et al. 2014). ...
Abstract
Linguistic data from South Asia identified several language isolates in the subcontinent. The Vedda, an indigenous population of Sri Lanka, are the least studied amongst them. Therefore, to understand the initial peopling of Sri Lanka and the genetic affinity of the Vedda with other populations in Eurasia, we extensively studied the high-resolution autosomal and mitogenomes from the Vedda population of Sri Lanka. Our autosomal analyses suggest a close genetic link of Vedda with the tribal populations of India despite no evidence of close linguistic affinity, thus suggesting a deep genetic link of the Vedda with these populations. The mitogenomic analysis supports this association by pointing to an ancient link with Indian populations. We suggest that the Vedda population is a genetically drifted group with limited gene flow from neighbouring Sinhalese and Sri Lankan Tamil populations. Interestingly, the genetic ancestry sharing of Vedda neglects the isolation-by-distance model. Collectively, the demography of Sri Lanka is unique, where Sinhalese and Sri Lankan Tamil populations excessively admixed, whilst Vedda largely preserved their isolation and deep genetic association with India.
... Based on our Bayesian analysis, we establish a time to the most recent common ancestor of 17,616 (95% HPD: 6661-32,561) for R30b2 (ESM_1, Fig. 6). Discrepancies were observed in earlier studies (Chaubey 2013;Ranaweera et al. 2014) regarding the distribution of R30 in the Vedda tribe on Sri Lanka. The observed R30 haplogroup distribution is mainly due to the exclusion of the diagnostic mutation at 373, which is one of the diagnostic mutations for R30 (van Oven and Kayser 2009). ...
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.
... Only a few genetic studies, including the mtDNA, Y and X chromosomes have been performed, and these confirmed the Sinhalese connection with mainland India. [22][23][24][25][26][27][28][29][30][31][32][33][34][35] Some studies have shown that the Sinhalese have a distinct origin, while a few of them suggested a connection with South Indian populations. 26,36 Analysis based on classical markers advocated a closer affinity of the Sinhalese population with South and West Indian populations than with the Bengalis. ...
... Genetic studies on the Sr ı Laṅk an population are mainly limited to haploid DNA markers. 22,39 The majority of Sr ı Laṅk an individuals studied so far showed an overwhelming presence of South-Asian-specific haplogroups. However, a significant presence of West-Eurasian-specific haplogroups has also been detected. ...
... The most common West-Eurasian mtDNA haplogroups are U7 and U1. 22,40 Thus, the West Eurasian connection of Sr ı Laṅk a appears likely. The lack of autosomal studies needs to be filled in order to understand the precise nature of peopling of Sr ı Laṅk a. ...
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.
... Mitochondrial markers were utilized to identify leopard coalescence and lineage sorting processes [1,30,49,51]. The mtDNA was used to address questions of genetic diversity, phylogeography, and population evolution within Asian leopards, especially the Sri Lankan leopard [52][53][54][55]. ...
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.
... Intriguingly, it has been documented that approximately 85,000 years ago, the first wave of human migration out of Africa followed the coast through the Middle East into Southern Asia via Sri Lanka (Kundu and Ghosh, 2015). Most importantly, the only precursor of modern human fossils in South Asia, dating back 37,000 years, was found in Sri Lanka (Ranaweera et al., 2014). ...
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".
... Genetic evidence of South Asians shows sustained isolation leading to genetic drift among small populations, differentiating groups such as the "Vedda" people from later agriculturalist settlers (i.e., Sinhala and Tamil) (Peiris et al., 2011;Ranaweera et al., 2014). However, while being characterised as a culturally distinct ethnic group, the "Vedda" or "Wannila Atto" (people of the forest) do not subsist primarily on hunting and gathering and speak an Indo-European language akin to Sinhala (Wijesekera, 1964;Dharmadasa, 1974). ...
... The possibility that Lanka was occupied by the earliest AASI groups migrating out of Africa but have not left genetic descendants is a possibility. The Eurasian (or ANI) links of the "Vedda" have been identified by many researchers (Howells, 1995;Peiris et al, 2011;Kulatilake, 2000;Ranaweera et al, 2014, Ranasinghe et al., 2015Kulatilake, 2020). In terms of cranial shape, the "Vedda" most closely resemble Dynastic Egyptians in (Howells 1995) and to North Indians and people from the Middle East such as Saudi Arabians (Kulatilake, 2000). ...
Sri Lanka’s rich palaeoanthropological and archaeological record as well as the present demographic aspects have much to offer in aiding our understanding of the island’s ancient past and recent population structure. Sri Lanka has yielded skeletal evidence for the earliest anatomically modern humans from South Asia indicating very early settlement of the region. Following early hunter-gatherer dispersals over 50,000 years ago, agricultural populations expanded to the region with historic settlements and urbanisation creating complex societies in the last three millennia. Through circum-Indian Ocean trade networks in historic times and colonial expansion in the last 500 years, population diversification has continued with groups of multiple genetic and ethno-linguistic backgrounds arriving and settling in the island. These early and later migrants share a gene pool that connects them to descendants of today, who form Sri Lanka’s multi-ethnic, multicultural, and multi-religious society. Using an anthropological perspective, this article investigates how complex societal and biological diversity would have developed over time in island Lanka. An appreciation of deep time, beyond historic records, helps us recognize that human evolution and diversification has been shaped over thousands of years, while an evidence-based, scientific approach is proposed to eliminate flawed ethnocentric interpretations.
... These include the earliest skeletal evidence for AMH in South Asia known as "Balangoda Man" (37 kya) [4], microfossils of several botanical taxa (47.8 kya) [5] and oldest microlithic technology in the region [6,7]. However, to date there are no data for ancient DNA from Sri Lanka, although a few studies have reported on contemporary populations, i.e.: Sinhalese, Sri Lankan Tamils, Sri Lankan Indian Tamils (with a very recent history in the island), Muslims (Moors), Malays, and the Adivasi (Vedda) [8,9]. ...
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.
