**Post has been updated with some corrections to the host information in the first phylogeny**
Today I am finally going to take a detailed look at the Nostoc phylogeny that I have been working on. But before I can begin, I have to figure out a way to highlight interesting taxa in an automated way. To do this, I wrote a script that adds html color tags after taxon names according to various classifications. While I was at it, I converted the branch support values to a binary system (≥0.9 vs. <0.9), which I can display as black circles on significantly supported branches. Note that this script requires that the tree be in NEXUS format rather than the plain Newick that is produced by PhyML. Opening the tree file in FigTree and saving it converts it to NEXUS, or the conversion could be scripted using Bioperl.
First, lets compare lichen photobionts to other free-living and symbiotic Nostoc strains:
../Scripts/ColourTree.pl ../Nostoc_rbcX_metadata.txt ../Nostoc_rbcX_host.nwk host >host_tree.nwk
As mentioned last time, the earliest branching taxa are free-living Nostoc isolates, along with a culture isolated from Peltigera, which I suspect may not be a true photobiont. There are also other free-living strains throughout the rest of the phylogeny that have been identified as N. edaphicum, N. calcicola, N. commune, N. muscorum and N. flagelliforme. Cyanobacterial taxonomy is a mess, but that is a topic for another day. There are also symbionts from a variety of plant groups throughout the main crown group including Cycads (Cycas, Macrozamia and Encephalartos), Bryophytes (Blassia and Anthoceros) and the angiosperm Gunnera. There are two cases where lichen photobionts are identical to plant symbionts (coloured black in the tree). Finally, there are two symbionts from Geosiphon pyriforme, a weird unicellular primative fungus, that hosts intracellular symbionts in sac-like, multinucleate cells (coloured red). There is some debate as to whether this symbiosis should be classified as a lichen or not.
Next, we can look at photobionts of different lichen families (the taxonomy of the lichen is based on that of the fungal partner):
../Scripts/ColourTree.pl ../Nostoc_rbcX_metadata.txt ../Nostoc_rbcX_host.nwk family >family_tree.nwk
At the deepest nodes in the tree, there is clearly a lot of host switching between different lichen families, but there is a lot of clustering of photobionts from the same lichen family at the tips of the tree. Photobionts of lichens in the Lobariaceae, Nephromataceae and Pannariaceae are all mixed up, which has been noted previously and has been proposed to reflect the ecological similarities of the hosts. There also appears to be a lot of historic photobiont sharing between lichens in the Peltigeraceae and the Collmenataceae, but such sharing is not ongoing as in all cases there are long branches separating photobionts of these families. Stereocaulon is the only species represented in the tree that is not part of the Peltigerales, an order of lichens that are universally associated with Nostoc, either as the sole photosynthetic partner or as a secondary photobiont. It would be interesting to see if other non-Peltigeralean lichens also associate with such divergent Nostoc genotypes.
Lastly, let’s take a look at species-level patterns. There is a lot of host switching among members of the same genus, but there do appear to be some species that are highly specialised:
../Scripts/ColourTree.pl ../Nostoc_rbcX_metadata.txt ../Nostoc_rbcX_host.nwk specialists >specialist_tree.nwk
With the current sampling, it is possible to identify four species of Leptogium and one each of Collema, Peltigera and Sticta that exclusively associate with a single cluster of photobionts, which is, in turn, exclusively associated with that lichen species (reciprocal specificity). Note that there is one P. malacea photobiont that falls out of the P. malacea cluster, but there are about four times as many specimens of this species as there are for any of the other specialists. As noted previously, these specialists predominate in the basal symbiotic Nostoc lineage.
There is a lot more that could be said about this tree, but I think I’ll leave it there for now. See this paper for a more detailed analysis of the complex photobiont specialisation patterns in Peltigera, including geographic patterns. On to the green algal photobionts in my next post…