Author Archives: heath.obrien

A preliminary look at host association patterns in Trebouxia

Having gone through the steps to build a phylogeny of the most common lichen photobiont, Trebouxia in my last post, I will now go on to discussing the host association patterns that it reveals. Here is the Trebouxia ITS tree … Continue reading

Posted in Green Algal Photobionts | Tagged | 1 Comment

Green Algal Photobionts: Trebouxia

Having beaten the phylogeny of symbiotic cyanobacteria into submission in my previous post, I am now tackling the green algae. My plan was to start with a big-picture analysis of 18S ribosomal RNA sequences, but my initial blast search returned … Continue reading

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An In-Depth Look at the Diversity of Symbiotic Nostoc

**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, … Continue reading

Posted in Cyanobacterial photobionts | Tagged | 4 Comments

Adding new sequences (Mistakes were made)

Looking through the tree produced in my last post, I noticed that several interesting sequences were missing from the tree. There are also less sequences in the tree than I get if I search for “Nostoc rbcX” in Entrez. Turns … Continue reading

Posted in Cyanobacterial photobionts | Tagged | 2 Comments

Adding host information to the Nostoc phylogeny

Having obtained 496┬áNostoc rbcX sequences (plus one outgroup) and used them to infer a reasonable phylogeny, all that is left is to assign host association information to the branches. This will require (a) parsing the sequence files to obtain host … Continue reading

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Obtaining the sequences

Perhaps not surprisingly given my background, I will be starting with Nostoc photobionts. In my opinion, the most useful marker for this group is rbcX, so I will be starting there. I have decided to use blast to obtain all … Continue reading

Posted in Cyanobacterial photobionts | Tagged | 1 Comment

Welcome to PhotobiontDiversity

As with most organisms, DNA sequencing has revolutionised our understanding of the genetic diversity and phylogenetic relationships of lichen photobionts over the last two decades. However, unlike most organisms, these insights have rarely been translated to formal taxonomic changes and … Continue reading

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