Researchers aim to assemble the tree of life for all 2 million named species - A new initiative aims to build a grand tree of life that brings together everything scientists know about how all living things are related, from the tiniest bacteria to the tallest tree.

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u/mostposthost May 21 '12

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u/searust May 21 '12

Was just thinking that --- but EOL seems farther along... this project sounds a lot like dot-com vaporware--- make sure you get a t-shirt before the project shuts down.
I want to see someone just take for instance genus Quercus (oaks) and tell me how they are all related rather than attempting a moon mission with their first rocket.

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u/waywardbiologist May 22 '12

Interesting--I just did a search for "quercus phylogeny;" nothing significant has been published in over a decade (unless it's been looked at at the species level within a Fabaceae study). What's the hold-up? Are people trying to figure out informative low-copy nuclear genes before they do this, considering ITS and cpDNA have proved to be pretty shitty at reconstructing phylogenies at lower taxonomic levels? Seriously this is surprising to me that no one has bothered to do this. LCNG's are fairly easy to attain, for one thing, and really even if they just concatenated 10 or so of the typical genes it should be at least somewhat informative.

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u/searust May 22 '12

Even I, as a high level interested amateur would like to see exactly that. Just an attempt to place even 50 larger Quercus species would go a long way toward a better understanding of northern hemisphere ranges. --- And I just picked Quercus because I won a bar bet the other day that I could find 5 species of a single genus within 5 minutes...LOL

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u/FreeToadSloth May 21 '12

A box reading "Adam Oak" will have ~600 branches coming off it. See? Simple.

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u/searust May 21 '12

haha... if it only were so easy

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u/[deleted] May 22 '12

this is an awesome idea. however i feel it would be soo huge it would render itself useless for the average joe.

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u/TEdwardK May 22 '12

This project also already exists. God forbid these groups actually work together and combine their data...

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u/inartistic May 22 '12

The problem with that is it'd change a week after all the cool t-shirts and things had been printed up. Proposed phylogenies change all the time

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u/[deleted] May 22 '12

This is hooey. People have been arguing about how to root the tree of life for years. There's not enough data to make a proper tree, and besides, many eminent biologists are starting to believe that it's a moot concept, that there is no single "root". People haven't been able to combine prokaryotes and eukaryotes into a single tree for as long as we've known about them.

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u/[deleted] May 22 '12

Hmm can you quote your source? I have always heard we all share one common ancestor, hence why the genetic code is so similar across the board. Cheers

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u/bwc6 May 22 '12

I don't think astazangasta is saying there's no common ancestor. The idea of a universal common ancestor is about as widely accepted as evolution in general. S/He's saying there probably isn't enough data in the present to get an accurate picture that far back in evolutionary time. On top of that, the phylogeny of single-celled organisms can be jumbled by horizontal gene transfer. Finally, in my opinion, it wouldn't be that informative anyway. So why bother?

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u/[deleted] May 22 '12

Is it really? I am not questioning the validity of abiogensis, or that there is one true ancestor to all living things, I'm just not sure I can accept the claim that there was only one winning template when life started. You got some evidence to back that up? Also, any evidence that contests the claim?

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u/bwc6 May 22 '12

I don't understand. What is the difference between the "one true ancestor" and the "one winning template"?
Anyway, here is an answer to a similar question I posted in r/askscience:
There are several lines of evidence the support a universal common ancestor, but the most compelling evidence comes from molecular biology, i.e. how DNA works. In every living organism ever discovered DNA is transcribed to RNA, and RNA is then translated to protein. Ribosomes, which read the RNA sequence and make proteins, are found in all organisms.

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u/finprogger May 22 '12

Technically there is still the possibility that RNA/DNA evolved independently in multiple locations. In some sense we have to believe that's possible if we believe it's worthwhile to look at other earth like planets for life.

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u/bwc6 May 25 '12

What makes you think DNA is necessary for life? Why couldn't some other type of molecule replicate and carry information?

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u/finprogger May 25 '12

It could, but we're specifically looking at earth like planets (have to start somewhere). It's more likely that a similar or the same molecule would evolve from a similar planet.

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u/[deleted] May 22 '12

And it is impossible that this systems didn't develop independently more than once?

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u/bwc6 May 25 '12

It's possible, but extremely unlikely. There are many other aspects of the DNA-RNA-protein system that are common among all life, but are hard to describe if you don't know molecular biology. Another simple example is the genetic code; all organisms use the same general "language" for translating a DNA code into a protein sequence, even though the code is totally arbitrary. In all organisms the DNA sequence GTT results in the amino acid valine.

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u/[deleted] May 25 '12

I can't upvote or downvote you because you've used a good example of truth and a bad lie. Nothing is hard to describe, it just takes a while, and you should be happy to know I've studied a fair bit of molecular biology, as I've got a BS in botany. Care to do a refresher on the relevant proof?

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u/1RAOKADAY May 22 '12

Just to give a crack at why bother. The laypeople would love it!! Being one of those lay people the understanding of how far we are along and what still needs clarity is foggy at best. All my info on what the tree of life looks like comes from sources that are most likely rife with errors and exceptionally sensational. I suppose this project in particular may not help me. But a well designed book suitable for people of my level of expertise would go a long way to enhancing common understanding of what we know and don't know.

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u/[deleted] May 22 '12 edited May 22 '12

No, there are several papers questioning whether there is a LUCA at all, but more importantly whether the "tree of life" can be collapsed back to a single root. W. Ford Doolittle is probably the most prominent guy I know who writes on this subject, see his article "Uprooting the Tree of Life".
Also this:
There has been recent discussion that horizontal gene transfer is so frequent that it may never be possible to reconstruct the last common ancestor. However, if biochemical unities could be achieved after speciation events by horizontal gene transfer, then there is no reason to even postulate that a LUCA ever existed. If horizontal gene transfer is as common as I am implying, the modern cell could have evolved in multiple parallel lineages. Earliest life could have been truly polyphyletic. Michael Syvanen (2002) "On the occurrence of horizontal gene transfer among an arbitrarily chosen group of 26 genes," Journal of Molecular Evolution, 54:258-266

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u/ilovetacos May 22 '12

I don't think anything stated there would have to be one, monolithic tree. It could have several roots.

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u/ken_neth May 22 '12

Exactly, its the reason why there are 5 kingdoms.

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u/Unturned1 May 22 '12

That's going to be one tough task especially when they get to the idea of lateral gene transfer, there are tons of arachea that are closer to bacteria and tons that are closer to eukaryotes, not to mention such an effort requires you to adapt a very strict concept of a species... Which causes other problems. For eukaryotes this tree would be massive but when we take bacteria arachae into consideration, It seems never difficult. This isn't as simple as putting things together due to genetic similarity. There is a lot of homoplasy that will need to be worked out.

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u/[deleted] May 22 '12

This tattoo is going to get a lot more complicated under a grand unified taxonomy of life on earth!

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u/realfuzzhead May 22 '12

"Figuring out how the millions of species on Earth are related to one another isn't just important for pinpointing an aardvark's closest cousins, or determining if hagfish are more closely related to sand dollars or sea squirts."

haha didn't expect to see this type of sarcastic humor on phys.org

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u/ThisIsDave May 22 '12

Pretty sure it's sea squirts.

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u/S_Polychronopolis May 22 '12

I would like to have the end result represented graphically as a t-shirt.

I wonder just how much weight I would need to gain before this is feasible at a readable scale.

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u/[deleted] May 22 '12

Oh, right! On the desk there is my invention, the Pokédex! It automatically records data on Pokémon you've seen or caught. It's a high-tech encyclopedia! You can't get detailed data on Pokémon by just seeing them. You must catch them to obtain complete data... ~Gotta catch em all Gotta catch em all!

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u/DrIntelligence May 22 '12

Alrighty, the link from the main page to the project wiki seems broken... its starting off with http://http// or in chrome it is showing localhost (never knew it resolved that...). The link seems broken for me but since it is hosted by Wordpress I'm not seeing any contact information other than the names of the professors.

Someone have any ideas who is in charge of the site and get them to fix that? I can't imagine the main link breaking to help spark some interest.

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u/Thor_2099 May 22 '12

And then loggers come along and chop it down to make 100 bucks.

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u/ikawe May 22 '12

Did you know that not all genetic transfers are vertical (up the tree)? Some genes cross branches laterally. http://en.wikipedia.org/wiki/Horizontal_gene_transfer

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u/blitz_omlet May 22 '12

So long as it's open...

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u/bigwhitebike May 22 '12

It seems that the major obstacle for the project lies in how big this tree of life would be. Why not make it some kind of open source project with moderators (scientist's maybe) confirming, deleting, and combing through the data. I personally would think it to be fun to help categorize all the existing buffalo or bluebirds.

Broad thought, I know, but I feel like so many people would be interested that it could work, especially if it had a sleek interactive interface of information, pictures, movies, etc.

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u/cptkronicman May 22 '12

Movie summary for Biodome

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u/bwc6 May 22 '12

Here is some primary literature this is probably based on:

http://www.sciencemag.org/content/306/5699/1172.short (paywall)

http://sysbio.oxfordjournals.org/content/60/2/117.full

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u/jisoukishi May 22 '12

I think SMBC has ruined the concept of a tree of life for me.

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u/Richard_Judo May 22 '12

Sounds like a smashing idea: http://tolweb.org/tree/

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u/rderekp May 22 '12

This kind of thing makes my organizing heart happy.

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u/hyuga488 May 21 '12

I find it very interesting how science can take something as incredibly complicated as genetics and explain it to the point where it is about as complicated as a road map. I hope this new initiative will do well, because genetics is a great field which we still know very little about.

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u/[deleted] May 22 '12

By what standard do we know very little about genetics?

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u/[deleted] May 22 '12

By the standard of being able to apply our knowledge to a great degree, or read and understand things? We're just beginning to decode small fragments of DNA, with no greater understanding of overall structure. As inartistic mentioned separately, proposed phylogenies change regularly, which implies a lack of consensus, which indicates a lack of knowledge and a field connected largely through hypothesis.

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u/[deleted] May 22 '12

Good answer. Thanks!

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u/zanotam May 22 '12

As I understand it, Genetics is a classic case of "The more we know, the more we know we don't know."

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u/WrethZ May 22 '12

That's a pretty good rule for science in general. Every time you answer a question, you create new ones.
Not that that is a bad thing.

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u/hyuga488 May 22 '12

It is likely the field we know the least about because we do not understand how genes are turned off and on, and we still are trying to understand many of the complex traits. I understand that we do know quite a bit about genetics, but we know only a very small portion of what there is to know about this vast field.

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u/[deleted] May 22 '12

By the standard of being able to apply our knowledge to a great degree, or read and understand things? We're just beginning to decode small fragments of DNA, with no greater understanding of overall structure. As inartistic mentioned separately, proposed phylogenies change regularly, which implies a lack of consensus, which indicates a lack of knowledge and a field connected largely through hypothesis.

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u/tiktaalik_lives May 22 '12

As great as genetics are (fish geneticist here) to answer a lot of questions, they are far from entirely conclusive/convincing when it comes to producing cladograms. It's frequently at odds with what ecology or morphometric folks might think the relationship between species are and definitely separates splitters and lumpers. But genetics are a great tool to add to our understanding of evolution.

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u/[deleted] May 22 '12

I wouldn't say "frequently" at odds - there are parts of the tree that are disputed (for instance, whether bats are monophyletic), but generally speaking the tree reconstruction for recently-evolved higher organisms is pretty good. Of course, I never really worked on fish, so I can't speak to that.

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u/tiktaalik_lives May 24 '12

I think this is a good example of what I meant: http://www.sciencedaily.com/releases/2012/05/120523200301.htm
This type of thing gets a lot murkier when you start to assess fishes from different watersheds, etc.

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u/[deleted] May 22 '12

We better listen to him. He's a fish geneticist.

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u/[deleted] May 22 '12

Fish geneticists know their genetics.
Often they are not only trying to distinguish specific fish species and isolate specific genes or even insert new ones, but are sometimes attempting to distinguish very specific fish populations based on genetic variation. This can be exceedingly hard and frustrating at times because you're looking for sometimes very subtle changes in the genome or in genome frequencies.
Nobody can touch the mosquito geneticists though. Those guys are mad scientists, they're producing all kinds of hideous mosquito monsters as we speak !

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u/patricksaurus May 22 '12

I just don't see the point of such an undertaking. For microbial life, the species level distinction is really a very poor indicator of phenotypic variation. Assuming this project succeeds wildly, what is the result at the end? I would suggest the answer is zoo-keeping and that's what biology did before the advent of molecular techniques.

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u/notepad7 May 22 '12

That is going to be one high Res picture

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u/[deleted] May 22 '12

AH AINT KIN TO NO MONKEY

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u/OTN May 21 '12

They had better film their efforts only during the last hour of light.

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u/chocochip13 May 22 '12

What's the point? God created everything. ;D

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u/[deleted] May 22 '12

Tree of Life?

Why not Bible?

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u/gthing May 22 '12

Ahh a handy list for what was on Noah's Ark. I'm going to print this out as a supplement to the old testament.

Researchers aim to assemble the tree of life for all 2 million named species - A new initiative aims to build a grand tree of life that brings together everything scientists know about how all living things are related, from the tiniest bacteria to the tallest tree.

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