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Moreover, mechanisms such as incomplete lineage sorting or complicated patterns of gene duplication and loss can lead to incompatibilities that cannot be represented on a tree.
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President Obama was even represented on a glass tree ornament on a small tree.
Overall genome content is not best represented on a single tree.
The orthologous relationships of the CesA genes between Setaria italica, barley (Hordeum vulgare), sorghum (Sorghum bicolor), Brachypodium distachyon and rice (Oryza sativa) are represented on a Bayesian phylogenetic tree (Additional file 1: Figure S1).
Additional file 1: Figure S2 shows values for the percent identity between GuaC from Enterococcus sp. 7 L76 and its closest homolog in other microbes represented on a bacterial phylogenetic tree [ 35].
It might have other features (other amino acids or other chemical pathways, for instance), it would not be descended from that ancestor, and it would be represented on another tree entirely.
Species for which tBLASTn querying did not yield hits are not represented on the tree.
This suggests that the association among these reactions is no artefact of their vertical co-inheritance among lineages represented on the tree.
Trypanosoma cruzi and T. brucei were used as out groups since these organisms are believed to diverge earlier than any other organism represented on the tree [ 46- 49].
Yet single gene trees are notoriously error prone and errors in the inference of LGT can be made when donor lineages are not represented on the tree (Beiko and Ragan 2009).
Note, that the absence of red circles does not indicate the absence of RFH genes in the corresponding bacteria, since the complete genome sequences of many bacteria represented on this tree are not available.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com