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Abstract
Background: It has now been well documented that the type (coding, non-coding) and location (nuclear, mitochondrial etc.) of genetic markers heavily influence evolutionary inferences; realistic assumptions can be drawn if multiple putatively neutral DNA fragments spread across the genome are used.
Aim: To infer human population history, Single Nucleotide Polymorphisms (SNPs), located in the non-coding regions of different genes in the X-chromosome have been developed as ‘putatively neutral markers’.
Subjects and methods: A population sample consisting of 16 male individuals from the western part of India was utilized for sequencing eight DNA fragments located in introns of three genes (Duchenne muscular dystrophy, Factor IX and Pyruvate dehydrogenase E1 sub-unit) on the human X-chromosome. PCR amplification and DNA sequencing confirmed the polymorphic status of all the fragments.
Results: Twenty nine SNPs were found to be segregating in the Western Indian population samples. Using these SNPs the nucleotide diversity and demographic parameters of the Western Indian population were estimated. Several tests of neutrality ascertained that all eight fragments evolve putatively neutrally. Further, linkage disequilibrium analyses confirmed this fact.
Conclusion: All eight DNA fragments seem to bear the characteristics to be considered as ‘putatively neutral genetic markers’ and thus, could be utilized for inference of human population and demographic histories.
Acknowledgements
The authors are thankful to all the human participants in the present study and the Indian Council of Medical Research (ICMR), New Delhi, India for intramural funding to Aparup Das. We thank the ICMR and the Council of Scientific and Industrial Research (CSIR), New Delhi, India for providing Senior Research Fellowships to Naazneen Khan and Anita, respectively. We also thank A. P. Dash, former Director of the National Institute of Malaria Research for facilities and encouragements, and the two anonymous reviewers for critical comments on an earlier version of the manuscript.
Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.