After a long hiatus, I’ve decided that it’s time to write some updates on the photobiont sequences that have been released over the last few months. I haven’t been entirely idle during the interim and have made a number of improvements to the workflow that I use to identify and analyze sequences. Metadata is culled from genbank files is now added to a database that’s accessible through the website and this information is then mapped onto the phylogeny automatically. I’ve written a shell script to carry out all steps of the analysis automatically, which is available here. A summary of all the steps is here, and all of the intermediate files are available here. Going forward, the most recent version of these files will be stored here.
A zoomable version of the Nostoc rbcX phylogeny can be viewed within the (modern) browser here, or you can download the pdf version. For each sequence type, name(s) of the host(s) that associate with those photobionts are indicated, along with the number of times that genotype has been sequenced. Names are colour coded according to the family of the lichen mycobionts, with all plant hosts coloured green (free-living strains are well, cyan). Circles on branches indicate aLRT values ≥ 0.9. I’ve highlighted new sequences in yellow.
Most of the sequences that have been added since my last post on Nostoc rbcX are from photobionts of aquatic species of Peltigera, all of which form two clades that are sister to groups of plant symbionts:
All of these sequences are from this paper (Miadlikowska et al. 2014), which used a multilocus sequencing approach to confirm that the monotypic genus Hydrothyria venosa (which was moved to the genus Peltigera in 2000) is actually a complex of three cryptic species. Peltigera hydrothyria is now the name for Hydrothyria venosa from eastern North America, while the lineage in British Columbia and Alaska has been renamed P. gowardii and the one in the Pacific Northwest of the USA has been renamed P. aquatica.
The photobionts of these three species form distinct lineages separate from all other lichen photobionts that have been sequenced (including hundreds of Peltigera photobionts from British Columbia). Interestingly, all of these sequences cluster together in the Miadlikowska tree, sister to the groups of plant symbionts in the top tree here. They didn’t include the Gunnera sequences which one of the P. hydrothyria groups clusters with here. They also excluded all of the spacer between the rbcL and rbcX genes. When I exclude the spacer, all of the aquatic Peltigera photobionts do cluster together, but they do not group with plant symbionts. Sequencing of additional loci will probably be necessary to resolve this question (Miadlikowska et al. did sequence 16S for some specimens, but not for any of the ones that form the second group in my analysis, and there is a P. hydrothyria 16S sequence from a previous study that does not group with theirs).
There is no sharing of photobiont genotypes between any of the aquatic Peltigera species. Miadlikowska suggest that this may indicate cospeciation, but the photobionts don’t form monophyletic groups for any of the species, which suggests to me that a lot of photobiont switching must have happened since speciation. The eastern North American species in particular associates with two very different lineages of Nostoc, either from different parts of the tree or on very long branches within the same lineage. It would be very interesting to sample more extensively in the area where the ranges of the western species overlap to see if photobiont sharing occurs there.
This was an interesting study and I hope it inspires folks to sequence photobionts form other aquatic cyanolichens, as well as free-living Nostoc from aquatic habitats. I’m hoping that it won’t take me months to update the other datasets that I’ve looked at here…
Miadlikowska, J., Richardson, D., Magain, N., Ball, B., Anderson, F., Cameron, R., Lendemer, J., Truong, C., and Lutzoni, F. 2014. Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes). American Journal of Botany 101:1141-1156.
Heath OBrien (2014). Photobionts of aquatic Peltigera. PhotobiontDiversity.org: http://dx.doi.org/10.6084/m9.figshare.1157389