Author Topic: Thank the sweet gods of biology  (Read 2353 times)

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Offline VainRobot

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Thank the sweet gods of biology
« on: September 19, 2015, 01:44:20 pm »
An initial draft has been released of an open source database that details the phylogeny of 2.3 million different species of organisms!

New Article

Scientific Article

Link to database (not very stable right now)

For people who have never studied or worked in biology, this is a huge deal. Doing phylogeny research has been a very frustrating process in the past for me. There's no central reliable source for information, especially for less common taxa or species. This is going to make my life that much easier. And hopefully aids research progress too!

Offline Ironchew

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Re: Thank the sweet gods of biology
« Reply #1 on: September 19, 2015, 04:08:03 pm »
Aron Ra was also working on a phylogeny database for a while now. At least up to this point, we haven't had a reasonably complete, up-to-date, and open-access list of species. Nice to hear that there are multiple people working on it.

I'm just hoping that the databases themselves use an open format so we don't have to reinvent the wheel.
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Offline Ultimate Paragon

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Re: Thank the sweet gods of biology
« Reply #2 on: September 19, 2015, 05:47:05 pm »
Simply amazing.

Offline TheL

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Re: Thank the sweet gods of biology
« Reply #3 on: September 22, 2015, 05:13:26 pm »
AWESOME!!  This is one of those things that us non-taxonomists just sort of assumed was around ages ago, simply because we couldn't believe it hadn't been implemented yet.

But when you mention just how many different species of organism are known...it must have been quite the undertaking, requiring years to complete.
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Offline Random Gal

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Re: Thank the sweet gods of biology
« Reply #4 on: September 22, 2015, 10:17:28 pm »
NOT. IMPRESSED.

Seriously, ABSOLUTELY NOTHING between crocodiles and birds? Sure, there was a "Theropoda" listed, but it ONLY CONTAINED EXTANT BIRDS!

And only a tiny handful of fossil organisms were included at all. For something purportedly showing the phylogeny of every lifeform on Earth, they just skipped over the ENTIRE HISTORY OF LIFE up until now?

This is what I hate about modern biology. Everything is genetics now. It's all about reading letters on a string and claiming that's all we need. Anything about the actual, visible history of life is tossed off as misleading and wrong because it's incomplete. It's estimated that 99% of all life on Earth is extinct, yet these people put together a phylogeny of the remaining 1% and claim everything is included? This is truly revolting.

EDIT: Tried searching the tree for "tyrannosaurus rex" "tiktaalik" "australopithecus" "mosasaurus" "basilosaurus" "ambulocetus" "archaeopteryx" "homo erectus" and "mammuthus" and got this:

Quote
This taxon is in our taxonomy but not in our tree synthesis database. This can happen for a variety of reasons, but the most probable is that it is flagged as incertae sedis.

If you think this is an error, please create an issue in our bug tracker.

"allosaurus" "diplodocus" "dunkleosteus" "triceratops" "dimetrodon" and "stegosaurus" returned no results at all.

FURTHER EDIT: Reading the scientific article, I could find nothing at all that mentioned fossil taxa, nor any reason to explain their exclusion from the tree. The article stated that a combination of molecular and morphological data was used, and that it largely incorporated existing phylogenies, so there was absolutely no reason to exclude fossil taxa at all.
« Last Edit: September 22, 2015, 11:10:08 pm by Random Guy »

Offline TheL

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Re: Thank the sweet gods of biology
« Reply #5 on: September 23, 2015, 10:54:44 am »
NO extinct taxa?  :(  That's kinda shitty.
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Offline rookie

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Re: Thank the sweet gods of biology
« Reply #6 on: September 23, 2015, 12:39:01 pm »
Can extinct species be added later?
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Offline Ironchew

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Re: Thank the sweet gods of biology
« Reply #7 on: September 23, 2015, 12:46:57 pm »
Can extinct species be added later?

Yeah, but the standards for that particular server seem to require several citations for the placement. Genes, while only salvageable from recently-living organisms, are an independent line of evidence that gives more certainty than the guesswork involved in placing fossils.

If they're keeping species out of the tree due to incertae sedis or uncertain placement, I'm guessing that's why.
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Offline Random Gal

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Re: Thank the sweet gods of biology
« Reply #8 on: September 23, 2015, 01:31:47 pm »
Can extinct species be added later?

Yeah, but the standards for that particular server seem to require several citations for the placement. Genes, while only salvageable from recently-living organisms, are an independent line of evidence that gives more certainty than the guesswork involved in placing fossils.

If they're keeping species out of the tree due to incertae sedis or uncertain placement, I'm guessing that's why.

According to the paper, they were using a combination of molecular and morphological methods. If they were only using genetics, I'd understand, but since they're using morphology in their classification it shouldn't have been a problem to include fossil taxa.

Offline Ironchew

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Re: Thank the sweet gods of biology
« Reply #9 on: September 23, 2015, 01:36:59 pm »
Can extinct species be added later?

Yeah, but the standards for that particular server seem to require several citations for the placement. Genes, while only salvageable from recently-living organisms, are an independent line of evidence that gives more certainty than the guesswork involved in placing fossils.

If they're keeping species out of the tree due to incertae sedis or uncertain placement, I'm guessing that's why.

According to the paper, they were using a combination of molecular and morphological methods. If they were only using genetics, I'd understand, but since they're using morphology in their classification it shouldn't have been a problem to include fossil taxa.

You're lucky to find a few bones of a given fossil specimen, though. Extrapolating that to the description of an entire species leaves uncertainties that this server would rather not include in the tree.

It's an open format, though. Anyone can make their own tree however they like it.
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Offline VainRobot

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Re: Thank the sweet gods of biology
« Reply #10 on: September 23, 2015, 03:37:08 pm »
I think it's important to note that this is a first draft. As stated in the paper:

Quote
This draft tree of life rep-resents an initial step. The next step in this community-driven process is for experts to contribute trees and annotate areas of the tree they know best.

They also noted that many of the included taxa are lacking a ton of necessary data:

Quote
Most tips in the synthetic tree are not represented by phylogenetic analyses

...

Many published relationships are not represented in the synthetic tree because this knowledge exists only as journal images.

At this point I think a joint effort between researchers who study extant and extinct organisms is required as well as a call for dissemination of unpublished phylogeny data.


Also, you can see the relationship between crocodiles and birds by looking at Archosauria.

Offline Random Gal

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Re: Thank the sweet gods of biology
« Reply #11 on: September 23, 2015, 07:35:25 pm »
Can extinct species be added later?

Yeah, but the standards for that particular server seem to require several citations for the placement. Genes, while only salvageable from recently-living organisms, are an independent line of evidence that gives more certainty than the guesswork involved in placing fossils.

If they're keeping species out of the tree due to incertae sedis or uncertain placement, I'm guessing that's why.

According to the paper, they were using a combination of molecular and morphological methods. If they were only using genetics, I'd understand, but since they're using morphology in their classification it shouldn't have been a problem to include fossil taxa.

You're lucky to find a few bones of a given fossil specimen, though. Extrapolating that to the description of an entire species leaves uncertainties that this server would rather not include in the tree.

It's an open format, though. Anyone can make their own tree however they like it.

I wasn't suggesting that anything known from "a few bones" should be included in the database. However, that is not the case with most of the taxa I would want to include.

Most of the taxa I mentioned above are complete enough to be used. Tyrannosaurus, Triceratops, Allosaurus, Diplodocus, Stegosaurus, Dimetrodon, Archaeopteryx, and Homo erectus are all known from multiple near-complete specimens.

Mammoths are even harder to explain, as is the Shasta Ground Sloth (Nothrotheriops), also missing. These are not only well known from complete remains, including soft tissue, but genetic data has been reported for both of them (frozen mammoths from Siberia, which recently allowed the complete genome to be sequenced, and ground sloth dung from a cave in California). There is an "Elephas primigenius" on the tree, which would appear to be the woolly mammoth, but sunk into the same genus as the Asian Elephant (which is tough to explain as the two lineages have been separate for 5 million years), but no Shasta Ground Sloth. Neanderthals are missing as well, despite the complete genome being available.

Australopithecus, Tiktaalik, and Ambulocetus are not as complete, but the important parts are there and their phylogenetic position is pretty clear from what's known. Moreover, I would argue that those three are so important to our understanding of evolution that it is a serious oversight not to include them.