Scientists Unveil New ‘Tree of Life’ | Hacker News Reader

Scientists Unveil New ‘Tree of Life’

nytimes.com

97 pointssrikar22 comments

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Original article: http://www.nature.com/articles/nmicrobiol201648

Link to higher-res image: http://www.nature.com/article-assets/npg/nmicrobiol/2016/nmi...

I think you meant to link to this for the better quality image:

http://www.nature.com/article-assets/npg/nmicrobiol/2016/nmi...

The NYT has a "super jumbo" diagram as well:

https://static01.nyt.com/images/2016/04/12/science/11TREEOFL...

Classic case where PNG would have been superior.

I'm always surprised at how much these articles play up the surprise factor of analyses like these. Are the results actually surprising to anyone in the field? It's a cool visualization and this represents an improvement over our older dataset. But not a shocking revelation.

It's fine to play up the conventional wisdom angle, but I don't like the pretense that the scientists themselves are surprised that eukaryotes amount to a tiny fraction of the diversity of life on earth.

Well put. Carl Woese figured this out back when sequencing 20 base pairs was a feat (now 20 million is routine). This paper seems to be fine-focus of his concepts using tools he'd only have dreamed of using in the 1970's. He's a hero.

To be fair, the tree plotting libraries are getting way better.

I had to really search on Wikipedia to understand this.

In case anyone else was just as confused as I was, have a read of:

1. https://en.wikipedia.org/wiki/Taxonomy_(biology)#Kingdoms_an...

2. https://en.wikipedia.org/wiki/Domain_(biology)

3. https://en.wikipedia.org/wiki/Kingdom_(biology)

Humans are part of the Eukaryote domain [a], in the Animalia kingdom. [b]

In terms of taxonomy, we are Verterbrates [c] of the Synapsid clade (branch) [d] of Chordates. [e] Within this we are mammalian [f] haplorhini [g] primates [h]. Within the primate order we are of the homonid family [i] and are classified as the species homo sapiens. [j]

a. https://en.wikipedia.org/wiki/Eukaryote

b. https://en.wikipedia.org/wiki/Animal

c. https://en.wikipedia.org/wiki/Vertebrate

d. https://en.wikipedia.org/wiki/Synapsid

e. https://en.wikipedia.org/wiki/Chordate

f. https://en.wikipedia.org/wiki/Mammal

g. https://en.wikipedia.org/wiki/Haplorhini

h. https://en.wikipedia.org/wiki/Primate

i. https://en.wikipedia.org/wiki/Hominidae

j https://en.wikipedia.org/wiki/Homo_sapiens

And together with fungi, we're classified in the Opistokonta clade in the article's tree.

https://en.wikipedia.org/wiki/Opisthokont

Life is awesome :-)

It's interesting that the three main domains of life are considered archaea, eukaryotes and bacteria; but looking at the diagram, the bacteria seem to be split into to two major clades that are more separated than even archaea and eukaryotes are.

So they've unveiled a new 'tree of life' for Bacteria.

We're in Opisthokonta, at the bottom right.

I know. I was referring to the new findings of the article.

it's weird how they use the term genomes over and over, but their reconstruction is based on ~12 RNA genes. There doesn't actually seem to be any genomics in this article.

To do this kind of very broad genomic analysis, you need a set of markers to compare. These markers, or easy identifiable orthologs, need to be present in most/all the organisms in the comparison.

Ribosomal RNA is a well studied marker for both prokaryotes and eukaryotes, so it makes sense to use these as markers.

yes, I'm aware of this (I studied under Noller who worked with Woese on this).

To do broad genomic analysis, you don't need any markers at all. markers are effectively pre-genomic sampling technology. You can obtain the rRNA without doing genomic sequencing. That's far cheaper and faster.

What you meant by "markers" are really "gene regions", and my point is that if you use 1% of the gene regions it's not genomic. And, further, the set that you want to compare is much larger than the ribosomal RNA. It should include the entire set of highly conserved genes that are common to all organisms, and even include a number of less conserved genes.

What's with the "Loki" and "Thor" references in the image?

This seems to answer that, was wondering the same thing myself.

http://www.science20.com/news_articles/is_loki_the_missing_l...

Loki. and Thor.?

Lokiarchaeota, they have many genes which code for proteins which aren't shared with other phyla: https://en.wikipedia.org/wiki/Lokiarchaeota

I found this interesting too. I'm thinking that is where the Norse Gods separated from the rest of the Eukaryotes.

Though they differ from us Eukaryotes in important ways, overall the Norse Gods represent a really stunning convergent evolution.

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