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The goal of this dissertation is to study the sequence polymorphism inretrotransposable elements of Entamoeba histolytica. The Quasispecies theory, aconcept of equilibrium (stationary), has been used to understand the behaviourof these elements. Two datasets of retrotransposons of Entamoeba histolyticahave been used. We present results from both datasets of retrotransposons(SINE1s) of E. histolytica. We have calculated the mutation rate of EhSINE1sfor both datasets and drawn a phylogenetic tree for newly determined EhSINE1s(dataset II). We have also discussed the variation in lengths of EhSINE1s forboth datasets. Using the quasispecies model, we have shown how sequences ofSINE1s vary within the population. The outputs of the quasispecies model arediscussed in the presence and the absence of back mutation by taking differentvalues of fitness. From our study of Non-long terminal repeat retrotransposons(LINEs and their non-autonomous partner's SINEs) of Entamoeba histolytica, wecan conclude that an active EhSINE can generate very similar copies of itselfby retrotransposition. Due to this reason, it increases mutations which givethe result of sequence polymorphism. We have concluded that the mutation rateof SINE is very high. This high mutation rate provides an idea for theexistence of SINEs, which may affect the genetic analysis of EhSINE1ancestries, and calculation of phylogenetic distances.

Analysis of Sequence Polymorphism of LINEs and SINEs in Entamoeba histolytica