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This hypothesis was supported by the high evolutionary rates exhibited by the few components still harboured by Apicomplexa.
In Arabidopsis, the reduced number of orthologs could also be explained by the high evolutionary distance from rice (i.e. eudicot vs. monocots).
However, the validity of conclusions drawn from both orthology assignment and phylogenetic tree reconstruction can be compromised by the high evolutionary rate particularly of microsporidian proteins (e.g., Brinkmann et al. 2005).
Although this situation may be explained by the existence of genes that are unique to the P. falciparum species, the Plasmodium genus or even the Apicomplexan phylum to which these organisms belong [ 5], it is certainly further exacerbated by the high evolutionary distance between P. falciparum and other sequenced organisms [ 6], which makes homology detection particularly difficult.
The functionality of the C-terminus is supported by the high evolutionary conservation not only in Aspergillus species (Supplementary Fig S1) but also for example in C. albicans with 41% identical amino acids in the C-terminal 66 amino acid residues (data not shown).
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Genes encoding for prototypical HSP70s were among the first genes to be cloned in Leishmania, because of their presumed importance in its life cycle, and also by technical reasons; that is, the high evolutionary conservation of HSP70 genes allowed their identification by hybridization using heterologous genes as probes (reviewed in [ 15]).
The high evolutionary rate may be the result of a nonsynonymous SNV in the mismatch repair gene mutS shared by P1L and all P2 isolates which conferred a hypermutation phenotype.
Hox-derived genes constitute the group with the highest evolutionary rate by all criteria.
This means that the higher evolutionary rate of M is not caused by the higher polymorphism in germ line mitochondria.
This may be explained by the very high evolutionary rates of these RNA viruses, leading to divergent strains at different localities over short periods and/or the lack of effective transmission between bank vole populations.
Of note, all three mutations are in highly conserved regions as evidenced by the high genomic evolutionary rate profiling score and thus are likely to be biologically significant.
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