
Scientists Unveil New ‘Tree of Life’ - srikar
http://www.nytimes.com/2016/04/12/science/scientists-unveil-new-tree-of-life.html
======
paulsutter
Original article:
[http://www.nature.com/articles/nmicrobiol201648](http://www.nature.com/articles/nmicrobiol201648)

Link to higher-res image: [http://www.nature.com/article-
assets/npg/nmicrobiol/2016/nmi...](http://www.nature.com/article-
assets/npg/nmicrobiol/2016/nmicrobiol201648/images_hires/w582/nmicrobiol201648-f1.jpg)

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

[http://www.nature.com/article-
assets/npg/nmicrobiol/2016/nmi...](http://www.nature.com/article-
assets/npg/nmicrobiol/2016/nmicrobiol201648/images_hires/w926/nmicrobiol201648-f1.jpg)

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

[https://static01.nyt.com/images/2016/04/12/science/11TREEOFL...](https://static01.nyt.com/images/2016/04/12/science/11TREEOFLIFE/11TREEOFLIFE-
superJumbo.jpg)

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guelo
Classic case where PNG would have been superior.

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skywhopper
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.

~~~
vibrio
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.

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chris_wot
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...](https://en.wikipedia.org/wiki/Taxonomy_\(biology\)#Kingdoms_and_domains)

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

3\.
[https://en.wikipedia.org/wiki/Kingdom_(biology)](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](https://en.wikipedia.org/wiki/Eukaryote)

b.
[https://en.wikipedia.org/wiki/Animal](https://en.wikipedia.org/wiki/Animal)

c.
[https://en.wikipedia.org/wiki/Vertebrate](https://en.wikipedia.org/wiki/Vertebrate)

d.
[https://en.wikipedia.org/wiki/Synapsid](https://en.wikipedia.org/wiki/Synapsid)

e.
[https://en.wikipedia.org/wiki/Chordate](https://en.wikipedia.org/wiki/Chordate)

f.
[https://en.wikipedia.org/wiki/Mammal](https://en.wikipedia.org/wiki/Mammal)

g.
[https://en.wikipedia.org/wiki/Haplorhini](https://en.wikipedia.org/wiki/Haplorhini)

h.
[https://en.wikipedia.org/wiki/Primate](https://en.wikipedia.org/wiki/Primate)

i.
[https://en.wikipedia.org/wiki/Hominidae](https://en.wikipedia.org/wiki/Hominidae)

j
[https://en.wikipedia.org/wiki/Homo_sapiens](https://en.wikipedia.org/wiki/Homo_sapiens)

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

[https://en.wikipedia.org/wiki/Opisthokont](https://en.wikipedia.org/wiki/Opisthokont)

~~~
chris_wot
Life is _awesome_ :-)

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xefer
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.

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

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jessaustin
We're in Opisthokonta, at the bottom right.

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

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dekhn
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.

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virusduck
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.

~~~
dekhn
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.

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weberc2
What's with the "Loki" and "Thor" references in the image?

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stuart78
This seems to answer that, was wondering the same thing myself.

[http://www.science20.com/news_articles/is_loki_the_missing_l...](http://www.science20.com/news_articles/is_loki_the_missing_link_in_the_evolution_of_complex_cells-155372)

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pc2g4d
Loki. and Thor.?

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

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

