  The goal of this dissertation is to study the sequence polymorphism in
retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a
concept of equilibrium (stationary), has been used to understand the behaviour
of these elements. Two datasets of retrotransposons of Entamoeba histolytica
have been used. We present results from both datasets of retrotransposons
(SINE1s) of E. histolytica. We have calculated the mutation rate of EhSINE1s
for both datasets and drawn a phylogenetic tree for newly determined EhSINE1s
(dataset II). We have also discussed the variation in lengths of EhSINE1s for
both datasets. Using the quasispecies model, we have shown how sequences of
SINE1s vary within the population. The outputs of the quasispecies model are
discussed in the presence and the absence of back mutation by taking different
values of fitness. From our study of Non-long terminal repeat retrotransposons
(LINEs and their non-autonomous partner's SINEs) of Entamoeba histolytica, we
can conclude that an active EhSINE can generate very similar copies of itself
by retrotransposition. Due to this reason, it increases mutations which give
the result of sequence polymorphism. We have concluded that the mutation rate
of SINE is very high. This high mutation rate provides an idea for the
existence of SINEs, which may affect the genetic analysis of EhSINE1
ancestries, and calculation of phylogenetic distances.
