All trees are BS! I usually start my talks about tree with some version of that phrase. Don’t despair to much. I will quality this. A lot of folks treat trees like they are real. They aren’t! Trees are mathematically models. And very useful mathematical models. Trees also help us reduced very complex environments and interactions into something that is visually easy to work with. Enough said on that.
Here is a mathematical model of the relationship of 16S RNA from some cyanobacteria. It’s broken down into genera. I used ITOL for the visualization of the tree and data overlay. I highly recommend ITOL for adding data to trees.
Copyright for the image:
What you are looking at is a neighbor-joined, 1000 bootstrapped phylogenetic tree of cyanobacteria 16S RNA at the genera level. Based on the mathematical model you choose for building trees you can make arguments about the relationships between the genera. You can also overlay data on the tree and make arguments for any patterns that might appear. Here ‘foo’ is overlaid onto the tree and there is no apparent pattern to the bars. There is a reason for this but that’s a topic you can read about in our paper.