Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India

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 F_ST 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.

Effects of caste, birth season, and family income on digit ratios

OBJECTIVES

The contributions of latitude and ethnicity in the determination of cross-society differences in digit ratios are unclear. In India, different castes (endogamous groups) have been living in the same areas (villages or towns) for the last 1500 years and, therefore, these groups may have different gene pools without a latitude-related difference component. Thus, in the present study, we studied the effect of caste on digit ratios. We also studied the effects of sex, birth season, and family income on digit ratios.

METHODS

We selected a sample of 301 college students (age: M = 19.9 years, SD = 2.63) in Muzaffarnagar city of western Uttar Pradesh, India, and asked participants for information regarding their birth month, religion, caste, and monthly family income. We measured participants' dorsal and palmar digit lengths (of all fingers, except the thumb, in both hands) using vernier calipers of 0.01 mm accuracy.

RESULTS

Other backward castes (intermediate castes) had longer digit lengths than general castes (upper castes), scheduled castes (lower castes), and Muslims. However, there was no difference in digit ratios of caste groups (scheduled castes vs. other backward castes vs. general castes vs. Muslims) or specific castes (Chamar-Jatav vs. Jat vs. Pandit-Tyagi). Winter-born women had lower left dorsal 2D:4D and 3D:4D ratios than summer-born women. Family income was related to higher dorsal 2D:4D and 3D:4D ratios among women. Moreover, in dorsal digit ratios, sex difference (men < women) occurred in digit ratios constituting digit 5, whereas, in palmar digit ratios, sex difference occurred in digit ratios constituting digit 2.

CONCLUSIONS

The present study suggests that endogamy-led genetic difference in ethnic/caste groups is not a determinant, whereas birth season (i.e., the exposure to sunlight) and family income might be determinants of digit ratios. In addition, compared to palmar digit ratios, dorsal digit ratios are better markers of sexual dimorphism.

Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

The South Asian subcontinent is characterized by a complex history of human migrations and population interactions. In this study, we used genome-wide data to provide novel insights on the demographic history and population relationships of six Indo-European populations from the Indian State of West Maharashtra. The samples correspond to two castes (Deshastha Brahmins and Kunbi Marathas) and four tribal groups (Kokana, Warli, Bhil and Pawara). We show that tribal groups have had much smaller effective population sizes than castes, and that genetic drift has had a higher impact in tribal populations. We also show clear affinities between the Bhil and Pawara tribes, and to a lesser extent, between the Warli and Kokana tribes. Our comparisons with available modern and ancient DNA datasets from South Asia indicate that the Brahmin caste has higher Ancient Iranian and Steppe pastoralist contributions than the Kunbi Marathas caste. Additionally, in contrast to the two castes, tribal groups have very high Ancient Ancestral South Indian (AASI) contributions. Indo-European tribal groups tend to have higher Steppe contributions than Dravidian tribal groups, providing further support for the hypothesis that Steppe pastoralists were the source of Indo-European languages in South Asia, as well as Europe.

Population Stratification and Underrepresentation of Indian Subcontinent Genetic Diversity in the 1000 Genomes Project Dataset

Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto–Burman (ATB) and Ancestral Austro-Asiatic (AAA). The 1000 Genomes Project (KGP) Phase-3 data include about 500 genomes from five linguistically defined Indian-Subcontinent (IS) populations (Punjabi, Gujrati, Bengali, Telugu and Tamil) some of whom are recent migrants to USA or UK. Comparative analyses show that despite the distinct geographic origins of the KGP-IS populations, the ANI component is predominantly represented in this dataset. Previous studies demonstrated population substructure in the HapMap Gujrati population, and we found evidence for additional substructure in the Punjabi and Telugu populations. These substructured populations have characteristic/significant differences in heterozygosity and inbreeding coefficients. Moreover, we demonstrate that the substructure is better explained by factors like differences in proportion of ancestral components, and endogamy driven social structure rather than invoking a novel ancestral component to explain it. Therefore, using language and/or geography as a proxy for an ethnic unit is inadequate for many of the IS populations. This highlights the necessity for more nuanced sampling strategies or corrective statistical approaches, particularly for biomedical and population genetics research in India.

Interleukin-1 gene cluster variants and recurrent pregnancy loss among North Indian women: retrospective study and meta-analysis

The aim of this study was to determine whether or not interleukin-1 alpha (IL-1a), interleukin-1 beta (IL-1b) and IL-1 receptor antagonist (IL-1RA) polymorphisms are associated with risk of unexplained recurrent pregnancy loss (RPL) among North Indian women. This retrospective case–control study examine 200 well-characterized RPL cases for IL-1 gene cluster variants, determined by restriction fragment length polymorphism-PCR. The observed allele, genotype and haplotype distributions were compared with those obtained from 300 ethnically matched negative controls. Invariant distribution of IL-1 gene cluster single-nucleotide polymorphisms was observed among RPL cases and controls. Meta-analysis of IL-1b _511, +3953 and IL-1RN 86-bp variable number tandem repeat from the reported literature and this study did not reveal any significant association with the risk of RPL. In conclusion, no significant difference between RPL and control groups was observed at the allele, genotype or haplotype levels when tested for association using the dominant, recessive and additive models of inheritance for IL-1 gene cluster variants. As far as is known, this is the first report from India pertaining to IL-1 gene cluster variants’ association with the risk of RPL from North India.

Magnetic resonance angiography findings in patients with ischemic stroke from North India

BACKGROUND

We sought to evaluate the magnetic resonance (MR) angiography (MRA) findings in patients with ischemic stroke (IS) from North India and correlate the changes with various conventional and nonconventional risk factors.

METHODS

The study took place at a tertiary care teaching hospital. The patients with IS were clinically evaluated including body mass index, dietary habits, and family history of stroke. MR imaging, MRA, and testing for blood sugar, lipid profile, B12, folic acid, and homocysteine were carried out. The MRA abnormalities were considered significant if stenosis was 50% or greater and these were categorized into extracranial (EC), intracranial (IC), or combined lesions. The location of infarct on MR imaging was also noted.

RESULTS

There were 151 patients whose median age was 60 (22-85) years. The EC MRA was abnormal in 56.3% and the IC MRA in 63.3% of patients, the internal carotid artery being the most common site. Corresponding infarct was present in 64.7% and noncorresponding in 45.3% of patients. The MRA abnormality positively correlated with hypertension and diabetes, and negatively with alcohol consumption. The EC MRA abnormality was more common in upper caste Hindus and Muslims and in the city dwellers.

CONCLUSION

In North Indian patients with IS, the frequency of EC and IC MRA abnormality lies between Whites and the Orientals.

Genetic polymorphisms of 15 STR loci in the population of the island of Cres (Croatia)

BACKGROUND

The population of the island of Cres presents one of the few persisting Eastern Adriatic isolates and is thereby suitable for human population differentiation analyses.

AIM

The aim of this study was to analyse the genetic structure of the island of Cres with respect to its eight sub-populations and to compare the genetic variation of the island of Cres with other Eastern Adriatic islands and the Croatian mainland.

SUBJECTS AND METHODS

Fifteen AmpFlSTR identifiler loci were analysed in a sample group of 122 unrelated autochthonous individuals from the island of Cres, Croatia.

RESULTS

Analysis of STR polymorphisms revealed genetic homogeneity among sub-populations of the island of Cres and small but significant levels of genetic heterogeneity among geographically distant Eastern Adriatic islands.

CONCLUSION

Despite a considerable degree of genetic homogeneity among the studied Eastern Adriatic islands, small but significant differentiation between distant islands indicates geographic sub-structuring which follows the isolation by distance model. This study is supportive of the notion that STR markers are useful for genetic differentiation between larger and geographically more distant regions.

Genetic variation in metabolizing enzyme and transporter genes: comprehensive assessment in 3 major East Asian subpopulations with comparison to Caucasians and Africans

The advent of high-throughput technologies has proven valuable in the assessment of genetic differences and their effects on drug activation, metabolism, disposition, and transport. However, most studies to date have focused on a small number of genes or few alleles, some of which are rare and therefore observed infrequently or lacked rigorous ethnic characterization, thus reducing the ability to extrapolate within and among populations. In this study, the authors comprehensively assessed the allele frequencies of 165 variants comprising 27 drug-metabolizing enzyme and transporter (DMET) genes from 2188 participants across 3 major ethnic populations: Caucasians, Africans, and East Asians. This sample size was sufficiently large to demonstrate genetic differences among these major ethnic groups while concomitantly confirming similarities among East Asian subpopulations (Korean, Han Chinese, and Japanese). A comprehensive presentation of allele and genotype frequencies is included in the online supplement, and 3 of the most widely studied cytochrome P450 (CYP) genes, CYP2D6, CYP2C19, and CYP2C9; 2 non-CYP enzymes, NAT1 and TMPT; and 2 transporter genes, SLCO1B1 and SLCO2B1, are presented herein according to ethnic classification.

Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci

The origin and relationships of Indian Muslims is still dubious and are not yet genetically well studied. In the light of historically attested movements into Indian subcontinent during the demic expansion of Islam, the present study aims to substantiate whether it had been accompanied by any gene flow or only a cultural transformation phenomenon. An array of 13 autosomal STR markers that are common in the worldwide data sets was used to explore the genetic diversity of Indian Muslims. The austere endogamy being practiced for several generations was confirmed by the genetic demarcation of each of the six Indian Muslim communities in the phylogenetic assessments for the markers examined. The analyses were further refined by comparison with geographically closest neighboring Hindu religious groups (including several caste and tribal populations) and the populations from Middle East, East Asia and Europe. We found that some of the Muslim populations displayed high level of regional genetic affinity rather than religious affinity. Interestingly, in Dawoodi Bohras (TN and GUJ) and Iranian Shia significant genetic contribution from West Asia, especially Iran (49, 47 and 46%, respectively) was observed. This divulges the existence of Middle Eastern genetic signatures in some of the contemporary Indian Muslim populations. Our study reveals that the spread of Islamic faith in the Indian subcontinent was predominantly cultural transformation associated with minor gene flow from West Asia.