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Author Topic:   Phylogeny
Member (Idle past 560 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008

Message 1 of 2 (826599)
01-04-2018 4:38 PM

I wanted to add this to the appropriate topic in links and information, but there isn't one, so I propose creating it.
As some may know, phylogenetics - the science of trying to reconstruct the tree of life - is a big interest of mine. And yet somehow I did not stumble across Hug et. al (2016) in Nature Microbiology until now. The article is called A new view of the tree of life; and is based on 16 ribosomal protein sequences; representing more than 3,000 organisms in total - including at least one example of every genus for which we have a full draft genome. They estimated a phylogenetic tree using Maximum Likelihood. The article is open access, so I hope I'm not violating anything by posting images here.
Below are two different representations of the tree generated; the first shows it as an unrooted network, and is included because it's pretty. The second shows a rooted tree in a more traditional representation; because I find that easier to read at a glance.
Things that leap out at me:
1. Animals, plants, fungi, slime moulds, and almost everthing you think of when you think of life is the little green section labelled as eukaryotes. That eukaryotes are a tiny splash in a sea of bacterial diversity is not new information; but it's still striking to see it presented like this.
2. Eukaryotes come out as very deeply nested within Archaea.
3. The Candidate Phyla Radiation - the huge purple bit making up the bottom third of the second image. A candidate phylum is a large, distinct group of bacteria known only from environmentally sampled DNA - meaning no one's ever isolated a cell from one of these buggers. I always assumed that these would be strewn around the bacterial tree of life; and while some candidate phyla are indeed nested amongst the well-known bacteria; the majority here form an enormous monophyletic group of mysterious organisms. This might partly be an artefact of the visualisation, but I can't help but come away from this feeling that we don't really know what one of the basic, primary groups of living organisms is.

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Message 2 of 2 (826601)
01-04-2018 5:18 PM

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