Synthetic tree

[Joseph Brown]

Here is a link to the newick of the synthetic tree created with "version3" of the subproblems.

https://www.dropbox.com/s/yu4vlceub1olf8r/Life_subprobsv3_synth_29April2015.tre.tgz?dl=0

It is also viewable on the tree browser.

There are 12 unsupported nodes:

Unsupported node MRCA of "Mayaca sellowiana ott1058573" and "Orectanthe sceptrum ott857925"
Unsupported node MRCA of "Oxyphyllum ulicinum ott643739" and "Proustia cuneifolia var mendocina ott367611"
Unsupported node MRCA of "Phtheirospermum parishii ott795571" and "Seymeria cassioides ott3882475"
Unsupported node MRCA of "Mortonia greggii ott755538" and "Zinowiewia australis ott483012"
Unsupported node MRCA of "Plagiopteron suaveolens ott623616" and "Zinowiewia australis ott483012"
Unsupported node MRCA of "Plagiopteron suaveolens ott623616" and "Denhamia viridissima ott458931"
Unsupported node MRCA of "Erophaca baetica subsp baetica ott812786" and "Glycyrrhiza astragalina ott88618"
Unsupported node MRCA of "Glycine pullenii ott932416" and "Phaseolus oblongifolius ott5533115"
Unsupported node MRCA of "Faxonella clypeata ott550672" and "Procambarus clarkii ott79864"
Unsupported node MRCA of "Stylocoeniella sp NOA-2005 ott250797" and "Siderastrea pliocenica ott3675249"
Unsupported node MRCA of "Stylocoeniella sp NOA-2005 ott250797" and "Hoplangia durotrix ott387485"
Unsupported node MRCA of "Agaricia undata ott1097550" and "Siderastrea pliocenica ott3675249"

HTH.

JWB.

[Mark Holder]

Thanks, Joseph.

Running the otcetera tool otc-check-taxonomic-nodes:

    otc-check-taxonomic-nodes -d Life_subprobsv3_synth_29April2015.tre supertree/step_1/taxonomy.tre

   

finds 23 cases of internal nodes in the tree that appear to be incorrectly labeled. This test compares the set of terminal taxa descending from the taxon in the synthetic tree to the set of terminal tax that are descendants of that taxon in OTT. The test does not check for clades in the synth tree that are unlabeled, but should have a label.

The full output is a bit verbose, listing the IDs that are extra or missing. I posted it at http://phylo.bio.ku.edu/ot/opentree3.0-check-taxonomic-nodes-output.txt

I think that this issue may be related to the unsupported nodes. An inspection of the unsupported nodes that Joseph mentioned (see below for longer output) shows that three come from subproblem ott712383 and one of the tips in that subproblem is the genus Siderastrea ott215891.  This is also one of the incorrectly labelled taxa (based on the  otc-check-taxonomic-nodes check).

There is an issue about this topic: https://github.com/OpenTreeOfLife/treemachine/issues/154

all the best,

Mark

output of otcetera/util/inspect_unsupported.py (which requires a very recent peyotl branch and the subproblems on the local fs):

########

Unsupported node MRCA of "Mayaca sellowiana ott1058573" and "Orectanthe sceptrum ott857925"

step_7_scratch/export-sub-temp/ott921871.tre contains the MRCA of the requested ids.

 1058573 appears as 1058573 in this subproblem.

 857925 appears as 857925 in this subproblem.

Unsupported node MRCA of "Oxyphyllum ulicinum ott643739" and "Proustia cuneifolia var mendocina ott367611"

step_7_scratch/export-sub-temp/ott46248.tre contains the MRCA of the requested ids.

 643739 appears as 643739 in this subproblem.

 367611 appears as 367611 in this subproblem.

Unsupported node MRCA of "Phtheirospermum parishii ott795571" and "Seymeria cassioides ott3882475"

step_7_scratch/export-sub-temp/ott23373.tre contains the MRCA of the requested ids.

 795571 appears as 795571 in this subproblem.

 3882475 appears as 97343 in this subproblem.

Unsupported node MRCA of "Mortonia greggii ott755538" and "Zinowiewia australis ott483012"

step_7_scratch/export-sub-temp/ott601168.tre contains the MRCA of the requested ids.

 755538 appears as 755538 in this subproblem.

 483012 appears as 483012 in this subproblem.

Unsupported node MRCA of "Plagiopteron suaveolens ott623616" and "Zinowiewia australis ott483012"

step_7_scratch/export-sub-temp/ott601168.tre contains the MRCA of the requested ids.

 623616 appears as 623616 in this subproblem.

 483012 appears as 483012 in this subproblem.

Unsupported node MRCA of "Plagiopteron suaveolens ott623616" and "Denhamia viridissima ott458931"

step_7_scratch/export-sub-temp/ott601168.tre contains the MRCA of the requested ids.

 623616 appears as 623616 in this subproblem.

 458931 appears as 806617 in this subproblem.

Unsupported node MRCA of "Erophaca baetica subsp baetica ott812786" and "Glycyrrhiza astragalina ott88618"

step_7_scratch/export-sub-temp/ott39538.tre contains the MRCA of the requested ids.

 812786 appears as 812786 in this subproblem.

 88618 appears as 88618 in this subproblem.

Unsupported node MRCA of "Glycine pullenii ott932416" and "Phaseolus oblongifolius ott5533115"

step_7_scratch/export-sub-temp/ott39538.tre contains the MRCA of the requested ids.

 932416 appears as 459704 in this subproblem.

 5533115 appears as 826181 in this subproblem.

Unsupported node MRCA of "Faxonella clypeata ott550672" and "Procambarus clarkii ott79864"

step_7_scratch/export-sub-temp/ott79861.tre contains the MRCA of the requested ids.

 550672 appears as 550678 in this subproblem.

 79864 appears as 79864 in this subproblem.

Unsupported node MRCA of "Stylocoeniella sp NOA-2005 ott250797" and "Siderastrea pliocenica ott3675249"

step_7_scratch/export-sub-temp/ott712383.tre contains the MRCA of the requested ids.

 250797 appears as 341609 in this subproblem.

 3675249 appears as 215891 in this subproblem.

Unsupported node MRCA of "Stylocoeniella sp NOA-2005 ott250797" and "Hoplangia durotrix ott387485"

step_7_scratch/export-sub-temp/ott712383.tre contains the MRCA of the requested ids.

 250797 appears as 341609 in this subproblem.

 387485 appears as 387485 in this subproblem.

Unsupported node MRCA of "Agaricia undata ott1097550" and "Siderastrea pliocenica ott3675249"

step_7_scratch/export-sub-temp/ott712383.tre contains the MRCA of the requested ids.

 1097550 appears as 1097550 in this subproblem.

 3675249 appears as 215891 in this subproblem.

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Mark Holder

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http://phylo.bio.ku.edu/mark-holder

==============================================

Department of Ecology and Evolutionary Biology

University of Kansas

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fax (shared): 785.864.5860

==============================================

[Cody Hinchliff]

Thanks Mark,

We took a look, and it seems like those 23 cases resulted from a bug in the way we were adding the missing children. Joseph is working on a solution now.