Evolutionary analyses of Plasmodium genomes
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Date
21/01/2020Author
MacLean, Oscar Alexander
Metadata
Abstract
Plasmodium is the genus responsible for causing malaria in humans, killing
more than 400,000 individuals a year. Species from the genus are also
capable of infecting different primate, avian and rodent species. In this thesis
I use previously published genomic data to investigate several aspects of
Plasmodium evolution. I compare mutation rates and the strength of selective
constraint across different subgenera of Plasmodium. I find little to no
conservation of mutation rate across the genus, and no evidence that these
mutation rate changes are driven by selective optimisation. I analyse patterns
of polymorphism in human-infecting and ape-infecting Plasmodium species,
looking for signatures of natural selection. Using this data, I find evidence for
a breakdown in the efficacy of purifying selection in the recent evolutionary
history of human-infecting species, but not in ape-infecting species. I suggest
this breakdown is caused by recent population expansions in the humaninfecting
populations. I investigate different methods to study the historic
selective regime of individual genes without being confounded by this recent
breakdown in the efficacy of purifying selection. I find strong evidence for
ongoing GC biased gene conversion in human-infecting Plasmodium vivax
from polymorphism patterns, and find evidence for this process in the
evolutionary history of species from other subgenera. I suggest the
differential strength of this process across the genus is responsible for the
wide range of genome GC contents found across different Plasmodium
species. Additionally, using the same polymorphism data, I find little evidence
for ongoing selection on codon usage in Plasmodium falciparum.