Phylogenetic Tree Of Sequenced Eukaryotes
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9.9 years ago
Lyco ★ 2.3k

The title says it all: does anybody know a source for a phylogenetic tree that contains as many completely sequenced eukaryotes as possible (and not too many other species). I do know sources that provide such trees for subgroups (filamentous fungi or green plants and such) and also 'giant trees' with thousands of species.

I would imagine that I am not the only one who could use a tree that focusses on species with completely sequence genomes, e.g. for phylogenomic reasoning.

Edit:

I am aware of the problem that some higher taxa cannot be places with certainty. This isn't really a big problem for my purpose, I could easily live with unresolved multifurcations or even with a collection of several unconnected subtrees. Here is the one that comes closest to what I need (except for the focus on sequenced organisms): skepticwonder.fieldofscience.com

My question focusses more on the fact if there are trees that show the relatioship between most fully-sequence organisms, not just a few representative members.

I am also aware of the problem that some sequences species are very closely related (which would require a finely resolved tree to separate them) while other eukarytotic groups are sparsely sampled. If I were to draw such a tree, I would probably give up on the high resolution but print multiple species names at the terminal nodes of the low-resolution tree.

phylogenetics tree • 4.3k views
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Re your edit: I edited my answer :)

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and another edit to my answer :)

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9.9 years ago

The problem is: There is no general agreement on the relative positions of the different kingdoms, and you will find articles the length of books by Thomas Cavalier-Smith.

Fig. 1 of Rogozin et al.

On the top level, I've been using the tree proposed by Rogozin et al.:

Fig. 4 of Rogozin et al.

The animal tree of life is also under debate, here's a proposal by Dunn et al..

If you don't care too much about the deep branches, you can use the NCBI taxonomy. (I once wrote some scripts to take the NCBI taxonomy and re-arrange some branches to resolve multifurcations). If you have a list of NCBI taxids and want to have a quick tree based on NCBI, I recommend iTOL.

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I am aware of these problems. However, this does not stop many evolutionary biologists from generating eukaryotic trees (with caveats). Here is the one that comes closest to what I need: http://skepticwonder.fieldofscience.com/search/label/Tree%20of%20Eukaryotes.

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Thanks, Michael. Are you aware of a tool that allows you to put in a number of NCBI TaxIDs and gives you a tree based on the NCBI taxonomy? If not, I could write one, shouldn't be too complicated.

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Thanks for your second edit! I wil check iTOL.

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There has been substantial progress on the relative placement of many of the supergroups (not kingdoms), although of course it isn't completely resolved, nor is the placement of the root.

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9.9 years ago

I would consider using the Interactive Tree of Life tool (iTOL : http://itol.embl.de). The global tree is described in the Ciccarelli (2006) paper : http://dx.doi.org/10.1126/science.1123061 and is made from completely sequenced genomes. You can provide a file with TaxIDs corresponding to the species you want to see on the tree and the rest of the tree will be pruned.

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9.9 years ago
Shigeta ▴ 460

Michael is right - some of the more resourced groups may keep their own database, drawn from calculations from rRNA or sets of conserved genes. still its tricky, and its supposedly easier to do this with bacteria than metazoans.

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9.9 years ago
DG 7.2k

If you focus only on completely sequence genomes the sampling problem is going to be important and can't be overlooked. Most diversity lies within the various supergroups composed entirely or almost entirely of microbial eukaryotes, and they are far less sampled than Archeplastida, Metazoans, and Fungi. There are phylogenomic trees out there that provide lots of coverage, and have all contributed to the tree you linked to from PsiWavefunction at SkepticWonder.

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