We’re not so different after all

  • New genetic testing reveals similarities in DNA of Lankans and other nationalities

BY Sumudu Chamara

As does the world, science too evolves, improving and sometimes debunking popular beliefs and findings, and it is this evolution that furthers the advancement of the human race. What it means to the public and the scientific community may vary; however, knowing people’s roots, and connections with other ethnic communities locally and internationally, is certainly a step towards understanding that the differences we see are sometimes not considerable, and that sometimes, we are not as different as we think we are.  

A recent local study has shown that all Sri Lankan ethnicities, except Indian Tamils clustered closely with populations from the Indian Bhil tribe, Bangladesh, and Europe, reflecting their shared Indo-Aryan ancestry. This was revealed after analysing 14 world populations against Sri Lankan ethnic groups. The study focused on reporting the X STR (X chromosomal short tandem repeat – a powerful complementary system used for paternity and forensic casework)-based population genetic information of all four main ethnicities in Sri Lanka for the first time, and also explaining the genetic substructure between Sri Lankan and several other global populations from South Asia, South East Asia and East Asia, Europe, Africa, and Brazil.

The study, titled “X chromosomal STR-based genetic polymorphisms (the inheritance of a trait controlled by a single genetic locus with two alleles [a variant form of a gene]) and the demographic history of Sri Lankan ethnicities and their relationship with global populations” was conducted by Genetech Sri Lanka Senior Scientist Nandika Perera, of the Open University of Sri Lanka’s (OUSL) Health Sciences Faculty; Gayani Galhena of the Colombo University’s Zoology and Environmental Sciences Department; and Gaya Ranawaka of the OUSL’s Health Sciences Faculty.

Through the study, 838 unrelated individuals, covering all four major ethnic groups in Sri Lanka, i.e. the Sinhalese, Sri Lankan Tamils, Indian Tamils, and the Moors, were successfully genotyped using a new 16 X STR multiplex polymerase chain reaction (PCR) system which has recently been developed for Sri Lankans. However, this system’s applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed so far.

The results had indicated a high forensic efficiency for the tested loci in all four ethnicities, confirming its suitability for forensic application on Sri Lankans, and the allele frequency distribution of Indian Tamils had shown subtle but statistically significant differences from those of the Sinhalese and the Moors, in contrast to frequency distributions previously reported for autosomal (genes in question are located on one of the numbered or non-sex chromosomes) STR alleles. 

According to the study report, these results suggest a sex-biased demographic history among Sri Lankans requiring a separate X STR allele frequency database for Indian Tamils. It further said that substantial differences observed in the patterns of linkage disequilibrium (LD) (non-random association of alleles at a pair of genetic loci), among the four groups, demand the use of a separate haplotype (a set of genetic determinants located on a single chromosome) frequency databases for each individual ethnicity. 

Adding that the genetic position occupied by each of the ethnic groups in Sri Lanka, both at the local and global scales, is not clear, owing to the demographic history and gene flow, the researchers claimed that the wide array of genetic markers currently available, provide an opportunity for reliably elucidating their genetic affinities.

“However, depending on the type of genetic markers used, the ancestral information of populations deduced from the analyses could be quite different, and each of these different approaches can complement each other with their characteristic genetic information,” they added.

The study involved analysing the genetic composition of Sri Lankan ethnicities in relation to other global populations, and allele frequencies were compared with 17 other world populations. For the study, depending on the availability of literature data, eight to 16 common X STR markers had been used. The results had shown that three populations from the South Asia region, i.e. the Bhil tribe and the Brahmin caste in India, Bangladesh, and Pakistan; two from populations from the South East Asia region, i.e. Malaysians and Thailand; three populations from the East Asia region, i.e. China, Japan, and Taiwan; five populations from the Europe region, i.e. Germany, Italy, Sweden, Denmark, and North Portugal; two populations from the Africa region, i.e. Somalia and Ivory Coast; as well as Brazil from Latin or South America were compared.

The study report explained: “Among the three South Asian populations, the Bhil tribe and the Brahmin caste populations of India are the most geographically proximal populations to Sri Lankan ethnic groups. Both these Indian populations did not show a significant genetic differentiation with the Sri Lankan ethnicities with respect to any of the tested loci. Similarly, the Bangladesh population also did not exhibit any population subdivision with the Sri Lankan ethnicities. However, the Pakistani population demonstrated significant differentiation from one or more ethnic groups of Sri Lanka in two loci out of the nine common loci compared.”

These results, according to researchers, suggest that the allele distribution of the four ethnic groups of Sri Lanka is very similar to the two tested Indian populations and the Bangladeshi populations, and that the Pakistani population too exhibits substantial similarity to Sri Lankan ethnic groups, even though not to the same extent of the Indian and Bangladesh populations. 

“On the contrary, the allelic distribution of many X STR loci in Sri Lankan ethnic groups differ from South East Asian, East Asian, European, and African populations, and among them, the East Asian and African populations are the most genetically distant populations to Sri Lankans,” the study report read.

Through studies conducted to further clarify the relationship between Sri Lankans and the world populations, the researchers had found that Sri Lankans were clustered together not only with Indians and Bangladeshis, but also with Europeans, and that Indian Tamils were placed towards the periphery of this main cluster, while South East Asians, East Asians, and Africans were placed at a distance, outside the main cluster. Results had shown similarity between 18 world populations including the four Sri Lankan ethnicities, i.e. the Sinhalese, Sri Lankan Tamils, Indian Tamils, and the Moors, and Bhil India, Bangladesh, Malaysia, Thailand, China, Japan, Taiwan, Germany, Italy, Sweden, Denmark, North Portugal, Somalia, and Ivory Coast.

“LD is generally expected to be high in populations, which are either small, reproductively isolated or have a low population growth. Indian Tamils who are tea estate workers, restricted mostly to the central part of the country, fit well into this description. In Sri Lanka, there are about 850,000 Indian Tamils, which had very limited genetic mixing with other populations due to social and cultural reasons. Nevertheless, only one loci pair among Indian Tamils showed LD according to our results. When considering the limited number of Indian Tamil samples used in the present study in calculating LD (63 males), it is possible that the low sample number may have masked the actual existence of LD among Indian Tamils. The same limitation is also valid for Sri Lankan Tamil and Moor ethnicities in which a similarly low level of LD were detected,” the study report said, adding that the high level of LD observed within the Sinhalese might have resulted from its largely admixed nature, and that all these facts highlight the requirement of a more exhaustive dataset with increased power to detect LD, before concluding on the true pattern of LD among Sri Lankan ethnicities.

According to the researchers, Indian Tamils were shown to have a subtle but statistically significant genetic subdivision from the Sinhalese, while the Sinhalese, the Sri Lankan Tamils, and the Moors, are highly panmictic (relating to a population in which mating is completely random, and any two individuals [male and female] are equally likely to mate). The study also noted that the two Tamil ethnicities, i.e. the Sri Lankan Tamils and the Indian Tamils, shared a common genetic background. 

Adding that the analysis had also supported an Indian origin for Sri Lankan Moors as suggested by some historians, the researchers noted that some of the analyses agree with the historical data on the early settlement of the four ethnic groups in Sri Lanka. 

It added: “According to anthropological and archaeological evidence, Sri Lankan Tamils have a very long history in Sri Lanka and have lived in the island since at least around the Second Century Before Christ. It is not surprising to see local female ancestry (analysed via the study) reflected among Moors via our X STR analysis, despite their Arabic origin, in light of the fact that the X chromosome spends two-thirds of its lifetime within females. Alternatively, the genetic similarity observed between the Sri Lankan Tamils and Moors may be reflecting the Indian origin of Moors as some scholars claim it to be. Likewise, the genetic similarity observed between the two Tamil populations might also lie in their common Indian origin. Since the X chromosome reflects more of the maternal bloodline, results reported in mitochondrial (mt) deoxyribonucleic acid (DNA) studies are also of much relevance to the present context. Despite that the number of mt DNA studies conducted on Sri Lankan ethnicities is very limited, the available reports closely agree with our observations and indicated a very fine genetic structure with a closer genetic relationship among the Sinhalese and the Sri Lankan Tamils, in comparison to that among the Sinhalese and the Indian Tamils. In addition, haplotype sharing between the Sinhalese and the Moors has also been demonstrated. When taken together with the fact that autosomal STR analysis have failed in detecting a genetic structure among the four ethnic groups, i.e. the Sinhalese, the Sri Lankan Tamils, the Indian Tamils, and the Moors, the results suggest a sex-biased demographic history for the Sri Lankan ethnicities.”

In conclusion, the study said that X chromosome-based population genetic data for all four major ethnic groups in Sri Lanka covers 99.5% of the total population, adding that the present study has also revealed subtle but statistically significant differences in X STR-based allele frequency distribution of the Indian Tamils with the Sinhalese and the Moors, contrary to the highly homogeneous genetic outlook portrayed by autosomal STR analysis. Claiming that this suggests a sex-biased demographic history for Sri Lankan ethnicities, the study report said that this observation recommends the use of a separate X STR allele frequency database for the Indian Tamils for forensic and kinship application purposes. 

The researchers further added: “In contrast, the observed genetic admixture present within the Sinhalese, the Sri Lankan Tamils, and the Moor ethnicities suggest the possible use of a common allele database for the purpose. Further, the genetic distances observed among the Sri Lankans and other nationalities in the world visualised in the myelodysplastic syndromes (MDS) (an onco-hematologic disease with distinct levels of peripheral blood cytopenias [a condition in which the number of blood cells declines], dysplasias [the presence of abnormal cells within a tissue or an organ] in cell differentiation, and various forms of chromosomal and cytogenomic [areas of chromosome biology in the genomic context] alterations) render evidence to the ancient linguistic origin of the Sri Lankan ethnicities – the Indo-Aryan origin of the Sinhalese and the Dravidian origin of the Tamil populations – which had been later affected to various degrees through genetic admixing between them. LD was detected along the X chromosome in all ethnic groups except the Sri Lankan Tamils, which needs to be considered during the likelihood calculations of kinship resolution and person identification. Further, the patterns of LD observed, which differ substantially among the four ethnicities, request the use of different haplotype frequency databases for the four ethnicities for forensic purposes.”

Moreover, even though the results of haplotype analysis suggest that the four studied X STR clusters can provide a powerful tool for kinship testing and relationship identification of Sri Lankan ethnicities, the researchers recommended that a more exhaustive sampling of the two Tamil groups and Moors is needed in order to confirm the LD and haplotype-based observations.

Even though The Morning attempted to contact Dr. Galhena to know how these findings would support the existing scientific experiments and the public, she was unavailable for comment.