1. Characterizing the genetic differences between Indo-European and Dravidian speaking Indian populations using a case/control based approach
Ranajit Das
Manipal Centre for Natural Sciences, Manipal University, Manipal, Karnataka, India
Introduction
Genetic admixture in modern Indian populations
Chromosome 15 shows highest SNP diversity .
India is a country with high ethnic and linguistic diversity. A strict caste system that existed in India for thousands of years have resulted in limited inter-caste marriages (exogamy) and thus limiting the gene flow among Indian populations from different castes and different states (Ali, et al., 2014). Modern Indian populations are descendants of two genetically diverged ancestral populations: Ancestral North Indians (ANI), which are genetically related to West Eurasians (people of Central Asia, the Middle East, the Caucasus, and Europe) and Ancestral South Indians (ASI), which according to some authors, are distantly related to indigenous Andaman Islanders (Reich, et al., 2009).
The major aim of this project is to interrogate the genome of ANI and ASI populations for SNPs that are significantly different between the two. I employed a case/control based approach dividing the Indian populations into two groups: ANI (control population) and ASI (case population) and investigated the genetic differences between the two.
- Log10(P)
Phenotypic association of the highly significant SNPs
Light skin: rs
Obesity: rs and rs
Smoking cessation: rs and others
Premature menopause: rs and rs244099
Waist circumference: rs
Schizophrenia: rs
ANI
Data sets
ASI
Siddi
Data borrowed from the Reich Lab, Department of Genetics, Harvard Medical School, Boston, USA.
Out of 378 individuals present in the original dataset, people of Andamanese, Austro-Asiatic, and Tibeto-Burman origin were removed and only Indo-European and Dravidian speaking people were kept (494,863 SNPs and N = 294).
Since Siddi people are descendants of Bantu people of Southeast Africa, they were excluded in the SNP analysis and the analysis was performed on 280 individuals (165 ASI and 115 ANI).
Population clusters
Ongoing and upcoming projects
Siddi population
Paniya population, Kerala
Jews_KE01 C2 C1 C2 C1
Jews_KE01
Vysya population, Andhra Pradesh
Paniya population, Kerala
Kamsali_191_R2
Ecological genomics and molecular evolution of fungus-growing, mound-building termites of India
Kashmiri Pandits, Jammu and Kashmir
Kashmiri Pandit
Chenchu population, Andhra Pradesh
A. Population clusters including Siddi
B. Population clusters excluding Siddi
2. Investigation of Anuran orders and families in Western Ghat region that survived through K-T mass extinction
Method
3. Big data in Biology: application in Evolutionary Biology
Population stratification was estimated using --cluster command in PLINK. Multidimensional scaling (mds) analysis was performed using --mds command alongside --read-genome flag. The ancestry of 294 samples (including Siddi people) was estimated using ADMIXTURE v1.3 . The Manhattan plot was generated in Haploview. mds plot and Q-Q plot were generated in R v The SNPs were annotated using SNPnexus web-based server.
4. Large mammal biodiversity
Summer Research Internship in Evolutionary MCNS Manipal University 2016
Acknowledgement
I thank Dr. Priya Moorjani of Department of System Biology, Columbia University for helping me obtaining the data from Broad Institute database.