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The Bushmen genomes are of particular interest since the Bushmen's ancestors branched off the main human lineage earlier than anyone else.
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The differentiation of the main human C. pneumoniae lineage from both the indigenous and animal lineages could be explained by adaptation of these strains to selective and antigenic pressure as a result of extensive antibiotic treatment regimes [ 52].
If the distinct phylogenetic clustering of SH511 and 1979 is a result of a separate zoonotic event to that of the main human C. pneumoniae lineage, then it is likely that the animal strain that they have evolved from is still unknown, and probably more similar to the frog DC9 strain in sequence and nucleotide content.
Although DNA methylation states at promoter regions have been highly conserved, these distal regions appear to have been the main reservoirs of epigenome divergence in the human lineage.
Our results show that in the mouse lineage, CpG odds ratio (the observed CpG frequency divided by the expected CpG frequency) is the main predictor of W→S substitution rates, which is not the case in the human lineage.
Viewed in this way, several of the most common fallacies in interpreting trees can arise: for example, that humans are the endpoint of a "main line," that there is a trend toward "human-ness" from left to right, that the human lineage includes a monkey ancestor, or that there has been no branching in the lineages leading to the other modern species of primates.
Shortly following the publication of the two competing genome papers, I led an effort to disprove one of the main findings in the other paper: that there had been over 200 bacterial genes transferred directly into the human lineage at some time in the past.
Possible pathways in the evolution of the human lineage.
According to the museum, humans ultimately evolved from a now-extinct ape, but human lineage and African great ape lineage diverged six to eight million years ago.
The same disposition could have been inherited down the human lineage.
Did that human lineage end in exile there — a genetic Siberia?
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com