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closeOnly slow evolving genes informative
Posted by ShiHuang on 17 Oct 2009 at 08:16 GMT
Your results are not all surprising. A new interpretation of DNA evolution suggests a distinction between slow and fast evolving genes (1,2). If you take a survey of the literature, you will find that those with similar results as yours tend to be enriched with fast evolving genes. I suggest that you redo the study using only proteins that show above 96% identity between mouse and dog. You will find that mouse and human forms a clade to the exclusion of dogs.
Ref.
1. Huang, S. Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers . Available from Nature Precedings <http://hdl.handle.net/101...> (2009)
2. Huang, S. (2009) Inverse relationship between genetic diversity and epigenetic complexity, Preprint available Nature precedings, http://precedings.nature....
3. Huang, S. (2008) Histone methylation and the initiation of cancer. Cancer Epigenetics, Ed. Tollefsbol, T., CRC Books.
RE: Only slow evolving genes informative
ginac replied to ShiHuang on 21 Oct 2009 at 13:36 GMT
We split the dataset into thirds and looked at the difference between genes evolving at long, medium and short evolutionary distances. The results are reported in Table 2 of this paper. The support for the human-dog topology does decrease with decreasing evolutionary distance although in this case all evolutionary distances supported the human-dog topology.