Biology subjects

Upadhyai, P.

Publications and source records attributed to Upadhyai, P..

4 recordsLinked to original sources

bioRxiv2017

Unraveling the population history of Indian Siddis

The Siddis are a unique Indian tribe of African, South Asian and European ancestry. While their ancestral origins have been traced to the Bantu populations from sub-Saharan Africa, their population history has remained an enigmatic question. Here, we have traced the biogeographical origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS). We evaluated 14 Siddi genomes in reference to 5 African populations from the 1000 Genomes project and 7 Bantu populations from the Human Genome Diversity project. GPS assigned the Siddi genomes to west Zambia and the present-day border between Zimbabwe and northeastern Botswana, overlapping with one of the principal areas of secondary Bantu settlement in Africa, ~1700 years before present (YBP). This is concordant with the secondary Bantu dispersal route from the east African Bantu center that brought the African ancestors of the Siddis to settlement sites in southeast Africa, from where they were disseminated to India, by the Portuguese. Our results also suggest that while the Siddi genomes are significantly different from that of the Bantus, they displayed the highest genomic proximity to the Luhyas and North-East Bantus from Kenya, and that ancestral Siddis are likely to have split from the Luhyas, ~2700 YBP, in congruence with known Bantu expansion and population migration routes. Together with historical, linguistic and anthropological evidences our findings shine light on the genetic relatedness between populations, fine-scale population structure and recapitulate the population history of the Siddis, in the ethnohistorical context of India.

evolutionary biology↗

bioRxiv2016

Tracing the biogeographical origin of South Asian populations using DNA SatNav

The Indian subcontinent includes India, Bangladesh, Pakistan, Nepal, Bhutan, and Sri Lanka that collectively share common anthropological and cultural roots. Given the enigmatic population structure, complex history and genetic heterogeneity of populations from this region, their biogeographical origin and history remain a fascinating question. In this study we carried out an in-depth genetic comparison of the five South Asian populations available in the 1000 Genomes Project, namely Gujarati Indians from Houston, Texas (GIH), Punjabis from Lahore (PJL), Indian Telugus from UK (ITU), Sri Lankan Tamils from UK (STU) and Bengalis from Bangladesh (BEB), tracing their putative biogeographical origin using a DNA SatNav algorithm - Geographical Population Structure (GPS). GPS positioned >70% of GIH and PJL genomes in North India and >80% of ITU and STU samples in South India. All South Asian genomes appeared to be assigned with reasonable accuracy, along trade routes that thrived in the ancient Mauryan Empire, which had played a significant role in unifying the Indian subcontinent and in the process brought the ancient North and South Indian populations in close proximity, promoting admixture between them, ~2300 years before present (YBP). Our findings suggest that the genetic admixture between ancient North and South Indian populations likely first occurred along the Godavari and Krishna river basin in Central-South India. Finally our biogeographical analyses provide critical insights into the population history and sociocultural forces driving migration patterns that may have been instrumental in shaping the population structure of the Indian subcontinent.

genomics↗

bioRxiv2016

Homozygous c.259G>A variant in ISCA1 is associated with a new multiple mitochondrial dysfunctions syndrome

The iron-sulfur (Fe-S) cluster (ISC) biogenesis pathway is indispensable for many fundamental biological processes and pathogenic variations in genes encoding several components of the Fe-S biogenesis machinery, such as NFU1, BOLA3, IBA57 and ISCA2 are already implicated in causing four types of multiple mitochondrial dysfunctions syndromes (MMDS) among other human diseases. MMDS are clinically characterized by neurodevelopmental delay, neurological deterioration, lactic acidosis, extensive white matter abnormalities and early death. We report on two unrelated families, with two affected children each with neurodevelopmental delay, regression of developmental milestones, seizures, extensive white matter abnormalities, cortical migrational abnormalities, lactic acidosis and early demise. Exome sequencing of two affected individuals, one from each family, revealed a homozygous c.259G>A variant in ISCA1 and Mendelian segregation was confirmed in both families. ISCA1 is a specialized factor known to mediate maturation of distinct Fe-S cluster (ISC) proteins. In silico functional analyses and structural modeling of the protein predict the identified ISCA1 variant to be detrimental to protein stability and function. Notably the phenotype observed in all affected subjects with the ISCA1 pathogenic variant is similar to that previously described in all 4 types of MMDS. The ISCA1 variant lies in the only shared region of homozygosity between the two families suggesting the possibility of a founder effect. To the best of our knowledge this is the first instance where ISCA1 deficiency has been shown to be associated with a human disease, a new type of multiple mitochondrial dysfunctions syndrome.

genetics↗

bioRxiv2016

Reconstruction of phylogenetic history to resolve the subspecies anomaly of Pantherine cats

All charismatic big cats including tiger (Panthera tigris), lion (Panthera leo), leopard (Panthera pardus), snow leopard (Panthera uncial), and jaguar (Panthera onca) are grouped into the subfamily Pantherinae. Several mitogenomic approaches have been employed to reconstruct the phylogenetic history of the Pantherine cats but the phylogeny has remained largely unresolved till date. One of the major reasons for the difficulty in resolving the phylogenetic tree of Pantherine cats is the small sample size. While previous studies included only 5-10 samples, we have used 43 publically available taxa to reconstruct Pantherine phylogenetic history. Complete mtDNA sequences were used from all individuals excluding the control region (15,489bp). A Bayesian MCMC approach was employed to investigate the divergence times among different Pantherine clades. Both maximum likelihood and Bayesian phylogeny generated a dendrogram: Neofelis nebulosa (Panthera tigris (Panthera onca (Panthera uncia (Panthera leo, Panthera pardus)))), grouping lions with leopards and placing snow leopards as an outgroup to this clade. The phylogeny revealed that lions split from their sister species leopard ~3 Mya and the divergence time between snow leopards and the clade including lions and leopards was estimated to be ~5 Mya. Our study revealed that the morphology-based subspecies designation for both lions and tigers is largely not valid. The estimated tMRCA of 2.9 Mya between Barbary lions and Sub-Saharan African lions depicts the restriction of female-mediated gene flow between the lion populations in the backdrop of the habitat fragmentation taking place from late Pliocene to early to mid-Pleistocene creating islands of forest refugia in central Africa.

evolutionary biology↗