Can anybody suggest an approach of testing the root for phylogenetic tree, for which one cannot add a reliable outgroup. We assume that the general topology of the tree is correct, but need to choose a first bifurcation event. The tree may contain both vertically and horizontally inherited sequences, what make the task more complicated.
Thanks
You could perhaps set up a few of dating analyses using different molecular clocks (strict, lognormal etc.) and with no root specified. The analysis will then find the best root itself, and the summary tree will provide support values for the two basal branches. It is crucial, though, that all hybrid sequences are identified and removed prior to analysis.
Actually, the datings/molecular clock - what I really don`t have to put the root properly (if I correctly understand what you are suggesting). I`m making a protein phylogeny. I have few deep branches, some of them containing archaeal sequences, some bacterial and some both without any branching similarity to the classical phylogenies, based on various markers as rRNA genes, ribosomal proteins etc. Thus, I need to understand which scenario of the protein appearance is most reliable: in LUCA, in a bacterium or in an archaeon (In all cases several HGTs have been occurred). I`m not sure I can do it using only this protein (trying now other proteins of the pathway), but probably I can test this phylogeny somehow (eg. from the knowledge of distribution of archaeal and bacterial sequences or using the lower taxa). Also, I`ve tried to find another proteins as a solid outgroup, but this also seems to be impossible since it is difficult to predict which activity appeared firstly.
btw, what do you mean by "hybrid sequences"? chimeras? Here, I`m working with well-approved native proteins, so it`s ok...
May be these papers can help with the question "which activity appeared firstly": Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Cotton & McInerney, PNAS, 2010.
Last acquisition of mitochondria by a host with chimaeric prokaryotic ancestry. Pittis & Gabaldon, Nature Letter, 2016.
Last one describe a relative simple method to construct a phylo-tree.
A list of relatively "old" and "new" families is suggested in "Rapid evolutionary innovation during an archaean genetic expansion", David & Alm, Nature Letter, 2011
What do you think about PAML as a phylogeny-tool?
One more
Algorithms for computing parsimonious evolutionary scenarios for genome evolution... Mirkin et al. BMC Evolutionary Biology, 2003
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