DnaSP | DNA Sequence Polymorphism and Genetic Diversity | Lecture 88 | Dr. Muhammad Naveed

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of DNA polymorphisms using data from a single locus (a multiple sequence aligned -MSA data), or from several loci (a Multiple-MSA data, such as formats generated by some assembler RAD-seq software). DnaSP can estimate several measures of DNA sequence variation within and between populations in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. Moreover, DnaSP can conduct a number of neutrality tests, such as (among other), the Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997), Ramos-Onsins and Rozas (2002), Achaz (2009) tests, and compute their confidence intervals by the coalescent. The results of the analyses are displayed on tabular and graphic form.

Results Interpretation
Genetic Diversity and Population Dynamics of Bacillus Anthracis
A total of 6 Haplotypes on the basis of the BslA gene of Bacillus anthracis were recognized in the study area. Bacillus anthrax contains a unique control region haplotype localized within the sub-population.
• Overall haplotype diversity; (Mean + SD) hd = 0.866 + 0.09
• Nucleotides diversity; pi = 0.299 + 0.358 was observed.
• FU’s Fs value (3.395) indicates that there is a deficiency of alleles or the population is facing bottleneck effects of genetic selection.
• overall positive Tajima’s D value (0.411) signifies the low level of both low and high-frequency polymorphism indicating a decrease in population size



About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)

With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 112 Research articles with 644 impact factors, 2500 citations, 01 book, and 03 book chapters. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
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