tag:blogger.com,1999:blog-37148773.post1153896232515698302..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Contradictory Phylogenies for CyanobacteriaLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-37148773.post-29736799624084219292015-11-15T15:53:42.720-05:002015-11-15T15:53:42.720-05:00Curious. The phylogeny of the Alphaproteobacteria ...Curious. The phylogeny of the Alphaproteobacteria (where the mitochondria originated from) has been highly problematic due to many members having a tendency to streamline their genome with a high degree of horizontal gene transfer: a streamlined genome may have allowed the protomitochondrion to form its symbiosys, but it is also problematic when genes are hastily concatenated en mass. I wonder if something similar is going on with cyanobacterial phylogeny, the living relatives of other organelle.Matteo Ferlahttps://www.blogger.com/profile/04090452288769979595noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61112372169449219052013-07-18T19:07:07.859-04:002013-07-18T19:07:07.859-04:00Larry,
How is it possible to trust neighbor-joini...Larry,<br /><br />How is it possible to trust neighbor-joining trees but not maximum likelihood trees? NJ is a rough estimate of a least squares fit tree, which is a maximum likelihood tree if the model of evolution you use to correct the distances is itself correct and without error. And NJ trees are known for weird artifacts if there are among-site rate differences and missing data.<br /><br />One possible explanation for differences among trees is taxon sampling. It might be biased in some way in one or more of the studies, or -- my personal favorite -- dense taxon sampling commonly gives an improved estimate of phylogeny, making the Shih et al. tree a better candidate. Horizontal transfer might be a problem, and there are ways to test for that; I recommend gene-jackknifing as a start.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.com