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Author Topic:   Phylogeny
Member (Idle past 567 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008

Message 1 of 4 (826600)
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.

Member (Idle past 567 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008

Message 3 of 4 (851808)
05-02-2019 4:01 PM

Phylogeny of eukaryotes
A post I meant to make months ago, but I realise I never did.
Eukaryotes (roughly, everything but bacteria) are sometimes classed into four groups - animals, plants, fungi and protists. Protists basically means 'everything else', and ever since the word was invented biologists have been aware that it's not a natural group. Electron microscopy enormously enhanced the understanding of how protists related to one another by allowing scientists to look at their sub-microscopic structure and find common features; leading to the naming of several groups which (unlike those based on gross morphology visible with a light microscope) are mostly believed to be monophyletic clades.
Only with the onset of molecular phylogenetics in the last couple of decades, though, did it finally become possible to start putting these different groups together into a proper family tree of life. There were several 'orphan' groups left over though, of uncertain placement. A few studies came out last year, however, that reckon they have finally figured out where these belong.
One named a group called CRuMs - the name being both an acronym of the constituent groups (Collodictyonidae, Rigifillidae, Mantamonas) and a reference to these obscure organisms being the little crumbs left over when everything else was divided into the big groups. CRuMs branch together somewhere near the split between amoebozoans and opisthokonts (the latter being the group which includes animals and fungi).
The final gap was filled in last year by the sequencing of mtDNA from two spironemids; the last remaining (well-characterised) protist group not included in molecular analyses. The researchers (as published in Lax et al, Nature vol 564, pages410-414 (2018)) found Spironemids to be very deep branching, the sister group to Diaphoretickes (an enormous group including most photosynthetic organisms, both plants and algae, along with all sorts of other stuff like forams, water moulds, some amoeba, malaria parasites etc etc). Their tree is below (spironemids are 'Hemimastigophora, since the authors decided the deep-branching position warranted a new 'phylum' level name):
We finally have a 'complete' tree of eukaryotic life. While I find this quite exciting, in reality the journey is not quite complete, for a few reasons:
1. While all the large groups have now been placed, there are still lots of orphan genera on uncertain placement (though many of these should probably be abandoned).
2. The above is only one interpretation. There is now broad agreement on most of the groups labelled above, and on their approximate position, but there is still a lot of uncertainty regarding specific branching order in some regions of the tree. The relationship among the main Diaphoretickes groups is particularly uncertain, possibly because many of these organisms have chloroplasts, which do not always shared the same evolutionary history as their host cells.
3. The position of the root is extraordinarily controversial, since there is no good outgroup to use to figure this out.
Some way to go, then, but I have been fascinated by how all life is related since I was a small child, and I am astonished how far scientists have come in figuring this all out since then. I'm still only in my thirties, and s have great hopes I'll see a lot more figured out.
Edited by caffeine, : No reason given.

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