Continuing with blog posts about my class EVE 161: DNA sequence based studies of microbial diversity.
Lecture 4 was fun and a bit scary for me. You see, I finally decided to read in detail – and cover in a course in detail – papers that claim that there are not three domains of life. Sure – there have been lots of papers suggesting this over the years. And I have read many of them. But somehow they did not convince me that it was time to teach about them in detail. In most course what I say is “Today, there is some controversy about whether the three domain tree of life of Woese is correct or not.” and I also frequently have said “And the rooted tree of life with Archaea being sister to Eukaryotes is also being debated” and then I say some namby pamby thing like “But for our purposes here the three domain tree is just fine”. But is it? Isn’t it time to at least show students some papers and findings suggesting that the three domain tree of life is being debated? I think so. And thus I sucked it up and decided to cover some such papers for this class.
The way I decided to do this was to have this class be about “The modern view of the tree of life” and cover two such modern papers. Paper 1 was Parfrey et al. 2010 on “Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life” – a wonderful paper in my opinion. This paper basically was used for two purposes – to see a better sampling of the diversity of eukaryotes. And to see how one goes about doing large scale phylogenomic analysis – how to deal with issues like concatenation, sampling more taxa, long branch attraction and so on.
And then paper 2 was Williams et al. 2012 A congruent phylogenomic signal places eukaryotes within the Archaea. It is a pretty thorough phylogenomics analysis that concludes in the end that the three domain tree was in essence an artifact of poor sampling and inappropriate evolutionary models. The conclude that the Eukaryotes should be placed within the Archaea and thus that the Archaea as they are known now are non monophyletic (that is, they do not all share a common ancestor to the exclusion of other organisms). The tree, according to their work, looks something like this:
I am still not 100% sure how I feel about their conclusions. But without a doubt they have convinced me that the three domain tree is not a foregone conclusion.
Anyway – here are the slides I used for the class.
There is no doubt in my mind that there is now doubt in my mind. That is good I think as it is fun to get people to think about how to resolve the patterns of evolution in the early evolution of major groups of organisms.