Are the 60 grouping in the synthetic tree without a source tree evidence of a bug?

Gordon and Ruchi reported (in their TreeOfLife_InformationSupport.docx in the https://drive.google.com/folderview?id=0B3yKYQFpnM_LQWRIY3UzQy01dVk&usp=sharing synthesis_paper folder) 60 groupings in the synthetic tree that do not appear to be backed by any source tree.

I know that this happens with many supertree methods (so it is not necessarily a problem per se). However, I thought (based on admittedly very limited knowledge) that: A. the synthesis step only highlighted edges in the "graph of life" to make a tree. B. each edge in the graph of life could be mapped to an edge in an input tree.

Either:

I've got something wrong about how treemachine works (quite plausible),
Gordon and Ruchi's notion of an edge in the synthesis tree being supported by a source tree edge differs from what I think of as a natural definition of that concept, or
there is a bug (in their scripts or treemachine).

thoughts?

I would need to know which nodes these are but my guess is that it would be due to placement of taxa once monophyly is broken. Just a guess though

On Fri, May 16, 2014 at 10:55 AM, Mark T. Holder notifications@github.comwrote:

Gordon and Ruchi reported (in their TreeOfLife_InformationSupport.docx in the https://drive.google.com/folderview?id=0B3yKYQFpnM_LQWRIY3UzQy01dVk&usp=sharingsynthesis_paper folder) 60 groupings in the synthetic tree that do not appear to be backed by any source tree.

I know that this happens with many supertree methods (so it is not necessarily a problem per se). However, I thought (based on admittedly very limited knowledge) that: A. the synthesis step only highlighted edges in the "graph of life" to make a tree. B. each edge in the graph of life could be mapped to an edge in an input tree.

Either:

I've got something wrong about how treemachine works (quite plausible),

Gordon and Ruchi's notion of an edge in the synthesis tree being supported by a source tree edge differs from what I think of as a natural definition of that concept, or

there is a bug (in their scripts or treemachine).

thoughts?

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/78 .

What @blackrim opines here sounds right to me. Be nice to have an explicit case to look at here.

Not sure if this is related, but there are some (at least one) unnamed nodes with out-degree 1 (e.g. https://tree.opentreeoflife.org/opentree/otol.draft.22@3864282) that it seems might be creating edges in Ruchi's list of conflicts. It looks like the node could be coming from taxonomy, (Eubrachyura), which is consistent with a phylogeny ranked highly in synthesis, pg _6227 6227 but is broken up by the lower ranked pg_2660 2660

Is that what @blackrim means by 'placement of taxa once monophyly is broken'?

My (not very well tested) code found 5 groupings in the synthetic tree for which I cannot find an edge/path in a source tree that supports them.

See the Results section below

It would be great if @ruchiherself could take a look at the results below, and send two descendants that are sufficient to identify any other problematic nodes (if we use the descendants in an MRCA query).

I don't understand how these nodes can get into the synthetic tree. But perhaps i'm just missing something about the synthesis. @blackrim , @josephwb , @chinchliff , any thoughts?

test set-up

Check out (or pull) a very recent copy of: NCL from https://github.com/mtholder/ncl

Set the env NCL_DIR to point to the top of your NCL build directory

cd to the trees-in-synth dir (downloadable from https://www.dropbox.com/sh/lnmcr208fk9gr1v/AABXBy7RcDOdtM233ZSavAUya/trees-in-synth?dl=0) so you have this structure: ./OpenTree.tre (from Ruchi equal to draftversion2.tre downloaded from dev resources site ) ./Taxonomy.tre (from Ruchi equal to Joseph's OTT_v2.8draft5_taxonomy-only.tre) ./mod_sourcetrees/ot##_##.tre (from Ruchi's source_trees - modified by removing all single quotes to make legal newick) ./mod_source_trees/tmp directory with output files that will be overwritten

testing taxonomic names.

Running:

$ "$NCL_DIR/example/check-taxo-node/checktaxonnodes" -frelaxedphyliptree OpenTree.tre Taxonomy.tre >check-tax-out.txt 2>check-tax-err.txt

produces warnings about nodes in the synthetic tree that have the wrong taxonomic assignment. Problems show up in the output redirection file. (at this point, the process exits cleanly even if there are problems noted in the file - this should change when we get this scripted into some sort of pipeline).

testing for nodes that are not supported by any tree

$ cd mod_source_trees
$ mkdir tmp
$ "$NCL_DIR/example/find-unsupported-edges/findunsupportededges" -frelaxedphyliptree ../OpenTree.tre ../Taxonomy.tre ./*.tre >../find-unsup-out.txt 2>../find-unsup-err.txt

What it does

it is not elegant, but it:

walks through the first arg (synth tree) registering pointers to the nodes parsing the taxon labels into OTT IDs
walks through the second arg (taxonomic tree) registering pointers to the nodes parsing the taxon labels into OTT IDs
for each input tree:
1. expand each leaf that is a not a tip in OTT to be a polytomy of all of the tips OTT IDs under that taxon.
2. mark the paths in the synth tree that are ancestral to any of the taxa in the expanded source tree
3. create a set of all of the MRCA sets in the source tree
4. walk through the marked edges of the synth tree. If you find a node with a MRCA set (with the taxa restricted to the leaf set of the source tree) and more than one of its children has an intersection with this leaf set, then the node is considered supported.
5. because nodes of out-degree 1 also show up in the synthetic tree (see https://github.com/OpenTreeOfLife/treemachine/issues/151), the program also marks and out-degree 1 direct ancestral path from a supported node as being supported as well.
walk through the synthetic tree and flag any unnamed nodes that are not supported. the taxonomy check should deal with the nodes contributed by taxonomy.

Results

I improved the output a little bit since posting to Dropbox, but the relevant results are the 5 problematic groupings:

Unsupported node ancestor 0 node(s) before MRCA of "Synechococcus rubescens ott4016821" and "Synechococcus_sp_JA-2-3B'a_2-13_ott893405"
Unsupported node ancestor 0 node(s) before MRCA of "Synechococcus sp PCC 7335 ott1039386" and "Acaryochloris ott673092"
Unsupported node ancestor 0 node(s) before MRCA of "Cyanothece aeruginosa ott636229" and "Acaryochloris ott673092"
Unsupported node ancestor 0 node(s) before MRCA of "Microcystis ott269068" and "SubsectionIII ott5246933"
Unsupported node ancestor 0 node(s) before MRCA of "Trichodesmium ott196997" and "Lyngbya ott878838"

where "0 node(s) before the MRCA" means that we are taling about the MRCA (not one of those funky out-degree one nodes).

some follow up

The README.txt in https://www.dropbox.com/sh/lnmcr208fk9gr1v/AADJTANQD1ykfg7Ud0Q6Lux9a?dl=0 is my notes on some additional (partially manual) follow up tests that make me think that the MRCA of "Trichodesmium ott196997" and "Lyngbya ott878838" in the synthetic tree is not supported by any of the 4 sources (pg_2542_5590, pg_2554_5580, pg_2739_6601, pg_2891_6699, or the taxonomy).

The URL with the graph ID is https://tree.opentreeoflife.org/opentree/otol.draft.22@3869643 but that does not load in the page correctly.

I have a list of tips that can serve as MRCA designators for problem cases from @ruchiherself (thanks!) Those are at: https://www.dropbox.com/sh/lnmcr208fk9gr1v/AACMTAetXqLMrUdcnsk2qea8a/trees-in-synth/problem-mrcas-from-ruchi.txt?dl=0

I think that the code base that she is using is to generate this list is https://github.com/ruchiherself/AssessSupertrees

The smallest (and therefore most promising for debugging) weirdness is the case of synthetic tree of life node 3846500

The problematic grouping is:

(Asterolinon_adoense_ott671286,(Anagallis_arvensis_subsp_arvensis_ott644217,Anagallis_monelli_ott671287))

Treemachine services list pg_50_1397 as supporting this group.

However, that tree this grouping:

(((Lysimachia_serpyllifolia_970630,Lysimachia_nemorum_990198),Asterolinon_adoense_671286),(Anagallis_monelli_671287,Anagallis_arvensis_486208))

This conflicts with the synthetic tree because it contains 2 species of Lysimachia inside the grouping of Asterolinon + Anagallis

In the output from gcmdr (given to me by Joseph and Ruchi - and posted in my dropbox folder linked above), the pg_50_1397.tre labels the clade containing Lysimachia_serpyllifolia_970630 and Lysimachia_nemorum_990198) with the genus name Lysimachia_635474. Consistent with that, there are no other Lysimachia in that input tree.

The only other tree that is used and includes Lysimachia is pg_2661 tree 6198. That study just has a tip mapped to the genus name (no info on whether or not the genus is monophyletic). That study does not have Asterolinon or Anagallis.

I would have expected pg_50_1397 to have moved the entire genus Lysimachia to be sister to Asterolinon_adoense_671286. But the genus just shows up as a monophyletic group supported by taxonomy in the polytomy of Primulace.

Asterolinon is on one of those annoying unconnected nodes. See this feedback which has links to https://github.com/OpenTreeOfLife/treemachine/issues/98 and https://github.com/OpenTreeOfLife/opentree/issues/310

I'm not sure why the checker that I wrote in NCL did not spot this case that Ruchi's code found. I'm going to investigate that right now.

Note I had the wrong "other" study using Lysimachia in the previous comment. I fixed it by editing that comment. the link is https://devtree.opentreeoflife.org/curator/study/view/pg_2661?tab=trees&tree=tree6198

OK there were some bugs in my script (primarily an early exit that caused the list of unsupported nodes to be cropped, but also a bug that cause the support to be inflated). My code is on the "ot" branch of NCL.
The findunsupportededges example app (if it is functioning correctly) confirms the 54 cases that Ruchi reported which involve nodes with out-degree > 1.

I may or may not be finding the nodes of out-degree=1 that her code finds. My code reports some. Her code reports 2, but her report does not allow me to find them.

So 2 of the "novel" groups, that my code finds may be the same as hers.

Overall my code finds 111 unsupported groups (output below).

I think that the Lysimachia case mentioned above is still the most promising lead.

@ruchiherself, it would be great if you could see why your code does not report the "Novel" groups listed below. It may be because my code is just looking for nodes which have no support in an input tree. I think that @ruchiherself's code just reports cases in which the grouping also conflicts with at least one input.

Thoughts on how to proceed are welcome.

Confirmation of unsupported node (designators =ott826450 ott1047333) ancestor 0 node(s) before MRCA of "Synechococcus rubescens ott4016821" and "Synechococcus_sp_JA-2-3B'a_2-13_ott893405"
Confirmation of unsupported node (designators =ott1039386 ott5258280) ancestor 0 node(s) before MRCA of "Synechococcus sp PCC 7335 ott1039386" and "Acaryochloris ott673092"
Confirmation of unsupported node (designators =ott5236290 ott5258280) ancestor 0 node(s) before MRCA of "Cyanothece aeruginosa ott636229" and "Acaryochloris ott673092"
Confirmation of unsupported node (designators =ott247513 ott301902) ancestor 0 node(s) before MRCA of "Microcystis ott269068" and "SubsectionIII ott5246933"
Novel unsupported node ancestor 0 node(s) before MRCA of "Trichodesmium ott196997" and "Lyngbya ott878838"
Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Calycocarpum ott124729"
Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Fibraurea ott477318"
Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Fibraurea ott477318"
Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Kolobopetalum ott522768"
Novel unsupported node ancestor 0 node(s) before MRCA of "Penianthus ott628586" and "Kolobopetalum ott522768"
Novel unsupported node ancestor 0 node(s) before MRCA of "Burasaia ott698917" and "Kolobopetalum ott522768"
Novel unsupported node ancestor 0 node(s) before MRCA of "Cucumis rumphianus ott313891" and "Cucumis melo ott1006256"
Novel unsupported node ancestor 0 node(s) before MRCA of "Umtiza ott723021" and "Acrocarpus ott1027571"
Novel unsupported node ancestor 0 node(s) before MRCA of "Barnebyella ott366943" and "Biserrula ott366947"
Confirmation of unsupported node (designators =ott767004 ott3919914) ancestor 0 node(s) before MRCA of "Sophora tonkinensis ott434824" and "Bolusanthus ott807796"
Confirmation of unsupported node (designators =ott767001 ott767004) ancestor 0 node(s) before MRCA of "Sophora tonkinensis ott434824" and "Cadia ott434088"
Confirmation of unsupported node (designators =ott359842 ott5532343) ancestor 0 node(s) before MRCA of "Baphia ott100710" and "Sophora japonica ott935514"
Confirmation of unsupported node (designators =ott3920796 ott5532343) ancestor 0 node(s) before MRCA of "Baphia ott100710" and "Isotropis ott382788"
Confirmation of unsupported node (designators =ott935514 ott3920020) ancestor 0 node(s) before MRCA of "Cladrastis parvifolia ott3920020" and "Sophora japonica ott935514"
Novel unsupported node ancestor 0 node(s) before MRCA of "Cladrastis parvifolia ott3920020" and "Cladrastis delavayi ott5457"
Confirmation of unsupported node (designators =ott799055 ott3919880) ancestor 0 node(s) before MRCA of "Ammodendron ott288771" and "Cadia ott434088"
Novel unsupported node ancestor 0 node(s) before MRCA of "Hymenaea ott31275" and "Cynometra ott330639"
Novel unsupported node ancestor 0 node(s) before MRCA of "Amherstia ott301507" and "Cynometra ott330639"
Novel unsupported node ancestor 0 node(s) before MRCA of "Brachystegia ott65504" and "Cynometra ott330639"
Confirmation of unsupported node (designators =ott671286 ott970634) ancestor 0 node(s) before MRCA of "Asterolinon adoense ott671286" and "Asterolinon linum-stellatum ott383202"
Confirmation of unsupported node (designators =ott644217 ott671286) ancestor 0 node(s) before MRCA of "Asterolinon adoense ott671286" and "Anagallis monelli ott671287"
Novel unsupported node ancestor 0 node(s) before MRCA of "Solanum aviculare ott494825" and "Solanum trisectum ott1026080"
Confirmation of unsupported node (designators =ott719936 ott779108) ancestor 0 node(s) before MRCA of "Stenostelma ott779109" and "Margaretta ott728333"
Confirmation of unsupported node (designators =ott150151 ott779108) ancestor 0 node(s) before MRCA of "Stenostelma ott779109" and "Asclepias multicaulis ott144808"
Novel unsupported node ancestor 0 node(s) before MRCA of "Xysmalobium ott779093" and "Pachycarpus ott119076"
Novel unsupported node ancestor 0 node(s) before MRCA of "Eriogonum ott942007" and "Coccoloba ott137596"
Novel unsupported node ancestor 0 node(s) before MRCA of "Phaeomegaceros squamuliger ott915124" and "Phaeomegaceros hirticalyx ott639740"
Novel unsupported node ancestor 0 node(s) before MRCA of "Hamacanthidae ott2841048" and "Axinella cf polypoides MCP03 144 ott26402"
Confirmation of unsupported node (designators =ott2839507 ott2839530) ancestor 0 node(s) before MRCA of "Suberitechnius ott2839508" and "Agelas clathrodes ott163384"
Confirmation of unsupported node (designators =ott121609 ott2839091) ancestor 0 node(s) before MRCA of "Polymastiidae ott623032" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304"
Confirmation of unsupported node (designators =ott121609 ott2841141) ancestor 0 node(s) before MRCA of "Trachycladidae ott526862" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304"
Confirmation of unsupported node (designators =ott2835934 ott2841141) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304"
Confirmation of unsupported node (designators =ott2841141 ott2841290) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Merliidae ott2841065"
Confirmation of unsupported node (designators =ott2837881 ott2841141) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Crambeidae ott644862"
Confirmation of unsupported node (designators =ott2837334 ott2837881) ancestor 0 node(s) before MRCA of "Amphilectus ott303949" and "Neopodospongia ott763487"
Confirmation of unsupported node (designators =ott2837479 ott2837881) ancestor 0 node(s) before MRCA of "Amphilectus ott303949" and "Isodictya compressa ott2837472"
Novel unsupported node ancestor 0 node(s) before MRCA of "Neoesperiopsis ott2837448" and "Isodictya compressa ott2837472"
Confirmation of unsupported node (designators =ott2837334 ott2837928) ancestor 0 node(s) before MRCA of "Diacarnus bismarckensis ott2837334" and "Neopodospongia ott763487"
Confirmation of unsupported node (designators =ott2837928 ott2837939) ancestor 0 node(s) before MRCA of "Strongylodesma ott2837927" and "Neopodospongia ott763487"
Confirmation of unsupported node (designators =ott2838257 ott5440746) ancestor 0 node(s) before MRCA of "Phellodermidae ott206663" and "Crambeidae ott644862"
Novel unsupported node ancestor 0 node(s) before MRCA of "Mycale titubans ott403492" and "Hymedesmiidae ott950042"
Novel unsupported node ancestor 0 node(s) before MRCA of "Tedaniidae ott962323" and "Hymedesmiidae ott950042"
Confirmation of unsupported node (designators =ott2835934 ott5440774) ancestor 0 node(s) before MRCA of "Spongosorites ott641040" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304"
Novel unsupported node ancestor 0 node(s) before MRCA of "Tylodesma informis ott5440774" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304"
Confirmation of unsupported node (designators =ott2839648 ott2839660) ancestor 0 node(s) before MRCA of "Sulcastrella ott2839649" and "Axinella cf polypoides MCP03 144 ott26402"
Confirmation of unsupported node (designators =ott2835466 ott2835496) ancestor 0 node(s) before MRCA of "Higginsia ott103935" and "Axinella cf polypoides MCP03 144 ott26402"
Confirmation of unsupported node (designators =ott2835574 ott2839151) ancestor 0 node(s) before MRCA of "Axinyssa cavernosa ott2835574" and "Sigmaxinella ott917215"
Confirmation of unsupported node (designators =ott2839151 ott2840284) ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Sigmaxinella ott917215"
Confirmation of unsupported node (designators =ott2839151 ott5448025) ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Hymeraphia ott303945"
Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Stelligera ott304841"
Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Paratimea sp BELUM GBR Mc6884 ott4938921"
Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Paratimea sp BELUM GBR Mc4323 ott4938924"
Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Higginsia mixta ott700742"
Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Halicnemia ott776728"
Confirmation of unsupported node (designators =ott253718 ott5448025) ancestor 0 node(s) before MRCA of "Raspailia uncinata ott5448025" and "Hymeraphia ott303945"
Confirmation of unsupported node (designators =ott5448024 ott5448025) ancestor 0 node(s) before MRCA of "Raspailia uncinata ott5448025" and "Ptilocaulis ott215104"
Confirmation of unsupported node (designators =ott303942 ott403483) ancestor 0 node(s) before MRCA of "Raspaciona ott828111" and "Tethyspira ott145572"
Confirmation of unsupported node (designators =ott303942 ott644861) ancestor 0 node(s) before MRCA of "Raspaciona ott828111" and "Aulospongus ott417668"
Confirmation of unsupported node (designators =ott172864 ott644861) ancestor 0 node(s) before MRCA of "Diacarnus spinipoculum ott644861" and "Aulospongus ott417668"
Confirmation of unsupported node (designators =ott644861 ott2841472) ancestor 0 node(s) before MRCA of "Diacarnus spinipoculum ott644861" and "Tetrapocillon ott2840942"
Confirmation of unsupported node (designators =ott695752 ott2835288) ancestor 0 node(s) before MRCA of "Raspailia phakellopsis ott695752" and "Ptilocaulis ott215104"
Confirmation of unsupported node (designators =ott670457 ott695752) ancestor 0 node(s) before MRCA of "Raspailia phakellopsis ott695752" and "Myrmekioderma granulata ott457665"
Confirmation of unsupported node (designators =ott670457 ott2837294) ancestor 0 node(s) before MRCA of "Axechina ott1027061" and "Myrmekioderma granulata ott457665"
Confirmation of unsupported node (designators =ott511196 ott2837294) ancestor 0 node(s) before MRCA of "Eurypon hispidum ott2837294" and "Myrmekioderma granulata ott457665"
Confirmation of unsupported node (designators =ott2837294 ott2841361) ancestor 0 node(s) before MRCA of "Eurypon hispidum ott2837294" and "Trikentrion ott172860"
Novel unsupported node ancestor 0 node(s) before MRCA of "Poicephalus ott225738" and "Psittrichas ott412122"
Novel unsupported node ancestor 0 node(s) before MRCA of "Poicephalus ott225738" and "Pionites ott682882"
Novel unsupported node ancestor 0 node(s) before MRCA of "Nannopsittaca ott667518" and "Pionites ott682882"
Novel unsupported node ancestor 0 node(s) before MRCA of "Mitu ott488150" and "Ortalis ott109892"
Novel unsupported node ancestor 0 node(s) before MRCA of "Mitu ott488150" and "Oreophasis ott488144"
Confirmation of unsupported node (designators =ott375229 ott3613449) ancestor 0 node(s) before MRCA of "Notopteris ott687489" and "Chironax ott99582"
Confirmation of unsupported node (designators =ott3613449 ott3613509) ancestor 0 node(s) before MRCA of "Notopteris ott687489" and "Dobsonia ott988790"
Confirmation of unsupported node (designators =ott201393 ott3613509) ancestor 0 node(s) before MRCA of "Epomophorini ott956035" and "Desmalopex ott268705"
Confirmation of unsupported node (designators =ott201393 ott3613485) ancestor 0 node(s) before MRCA of "Melonycteris ott687488" and "Desmalopex ott268705"
Novel unsupported node ancestor 0 node(s) before MRCA of "Pteropus aruensis ott3613485" and "Desmalopex ott268705"
Novel unsupported node ancestor 0 node(s) before MRCA of "Pteropus aruensis ott3613485" and "Pteropus capistratus ott609464"
Novel unsupported node ancestor 4 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"
Novel unsupported node ancestor 3 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"
Novel unsupported node ancestor 2 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"
Novel unsupported node ancestor 1 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"
Novel unsupported node ancestor 0 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"
Novel unsupported node ancestor 0 node(s) before MRCA of "Pseudosimochromis ott1089695" and "Limnotilapia ott303029"
Novel unsupported node ancestor 0 node(s) before MRCA of "Sphyraenidae ott280947" and "Istiophoriformes ott5554905"
Novel unsupported node ancestor 0 node(s) before MRCA of "Cirrhitiformes ott930720" and "Acanthuriformes ott515461"
Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Lagocephalus ott986279"
Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Chelonodon ott95360"
Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Chonerhinos ott3631233"
Confirmation of unsupported node (designators =ott974751 ott3627699) ancestor 0 node(s) before MRCA of "Serpenticobitidae ott5551560" and "Tanichthys ott306827"
Confirmation of unsupported node (designators =ott125135 ott3626575) ancestor 0 node(s) before MRCA of "Labeo ott160620" and "Tanichthys ott306827"
Novel unsupported node ancestor 0 node(s) before MRCA of "Raiamas ott837023" and "Tanichthys ott306827"
Novel unsupported node ancestor 0 node(s) before MRCA of "Leptobarbus ott653127" and "Tanichthys ott306827"
Confirmation of unsupported node (designators =ott598619 ott5003672) ancestor 0 node(s) before MRCA of "Dorylaimia ott5424357" and "Isolaimida ott658328"
Novel unsupported node ancestor 3 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506"
Novel unsupported node ancestor 2 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506"
Novel unsupported node ancestor 1 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506"
Novel unsupported node ancestor 0 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506"
Confirmation of unsupported node (designators =ott2981100 ott4668275) ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Raninoidea ott233901"
Confirmation of unsupported node (designators =ott4668275 ott4668960) ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Corycodus ott38070"
Novel unsupported node ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Majoidea ott428460"
Novel unsupported node ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Portunoidea ott757096"
Novel unsupported node ancestor 1 node(s) before MRCA of "Panopeidae ott938012" and "Portunoidea ott757096"
Novel unsupported node ancestor 0 node(s) before MRCA of "Panopeidae ott938012" and "Portunoidea ott757096"
Confirmation of unsupported node (designators =ott4667880 ott4668095) ancestor 0 node(s) before MRCA of "Panopeidae ott938012" and "Xanthidae ott757095"
Confirmation of unsupported node (designators =ott722710 ott2978847) ancestor 0 node(s) before MRCA of "Eriphiidae ott45361" and "Xanthidae ott757095"
Novel unsupported node ancestor 1 node(s) before MRCA of "Dairidae ott531267" and "Carpiliidae ott677778"
Confirmation of unsupported node (designators =ott677780 ott722710) ancestor 0 node(s) before MRCA of "Dairidae ott531267" and "Carpiliidae ott677778"

Final summary:
203700 internal nodes were named in the reference tree. These were not rigorously checked against the taxonomy. They may not be detected as errors.
35755 internal nodes where flagged as being supported by an input (including taxonomy).
    12477 of these were named (some of the support could just be the taxonomic expansion of tips).
    23278 of these were unnamed.
111 unsupported nodes.

When we started this discussion a week ago the focus was primarily on whether it is possible to have unsupported nodes in the synthetic tree. So it wasn't really that important to count how many such nodes are there. I tried to get to the bottom of it today.

Following Wilkinson et al. (2005), an internal node (or grouping) 'v' of the synthetic tree is in support, conflict, permit, or irrelevant against an input tree 'T'. (One and only one of these four is true for each node against an input tree.) Let C(v) is the set of leaves under 'v' in the synthetic tree. Now if C(v) and 'T' do not share more than 1 leaf then 'v' is irrelevant with respect to 'T'. If 'T' has a node 'u' such that all the leaves under 'u' are also present in C(v) and C(v) doesn't have any other leaf of 'T' then 'v' is supported by 'T', or if one resolution in 'T' can produce a node like 'u' then 'T' permits 'v'. If none of these applies then 'v' conflicts with 'T'.

Notice that when the synthetic tree is studied against taxonomy along with other trees, it is never the case that a node in the synthetic tree is irrelevant with respect to all the input trees (total 485 trees = 1 taxonomy + 484 other trees). So it boils down to conflict, support, and permit.

56 conflicting nodes that I reported earlier are those nodes in the synthetic tree that only conflicts (no support or permit) with the input trees (if they are relevant). I find these nodes most disturbing so I suggested to report them in the paper.

If I stop giving the benefit of ignorance and start penalizing for permit, then the numbers go up. For example, if I count the nodes that do not get any support (i.e., the nodes that have only conflict, permit, or irrelevant) then there are 87 such nodes (more details attached).

I help in reaching to the degree 2 (or out-degree=1) nodes in this sheet. These two nodes should be the parents of the resulting MRCAs.

I am trying to think about 111 unsupported nodes reported by Mark, or 24 missing nodes (111 nodes by Mark - 87 node by me). By the way, why multiple "Novel" nodes point to the same MRCA , e.g., 1) MRCA of "Simochromis ott710023" and "Limnotilapia ott303029", 2) MRCA of "Lomoidea ott389510" and "Eumunida ott389506" appear multiple times?

Cheers, Ruchi

On Thu, Jan 29, 2015 at 8:54 AM, Mark T. Holder notifications@github.com wrote:

OK there were some bugs in my script (primarily an early exit that caused the list of unsupported nodes to be cropped, but also a bug that cause the support to be inflated). My code is on the "ot" branch of NCL.

The findunsupportededges example app (if it is functioning correctly) confirms the 54 cases that Ruchi reported which involve nodes with out-degree > 1.

I may or may not be finding the nodes of out-degree=1 that her code finds. My code reports some. Her code reports 2, but her report does not allow me to find them.

So 2 of the "novel" groups, that my code finds may be the same as hers.

Overall my code finds 111 unsupported groups (output below).

I think that the Lysimachia case mentioned above is still the most promising lead.

@ruchiherself https://github.com/ruchiherself, it would be great if you could see why your code does not report the "Novel" groups listed below. It may be because my code is just looking for nodes which have no support in an input tree. I think that @ruchiherself https://github.com/ruchiherself's code just reports cases in which the grouping also conflicts with at least one input.

Thoughts on how to proceed are welcome.

Confirmation of unsupported node (designators =ott826450 ott1047333) ancestor 0 node(s) before MRCA of "Synechococcus rubescens ott4016821" and "Synechococcus_sp_JA-2-3B'a_2-13_ott893405" Confirmation of unsupported node (designators =ott1039386 ott5258280) ancestor 0 node(s) before MRCA of "Synechococcus sp PCC 7335 ott1039386" and "Acaryochloris ott673092" Confirmation of unsupported node (designators =ott5236290 ott5258280) ancestor 0 node(s) before MRCA of "Cyanothece aeruginosa ott636229" and "Acaryochloris ott673092" Confirmation of unsupported node (designators =ott247513 ott301902) ancestor 0 node(s) before MRCA of "Microcystis ott269068" and "SubsectionIII ott5246933" Novel unsupported node ancestor 0 node(s) before MRCA of "Trichodesmium ott196997" and "Lyngbya ott878838" Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Calycocarpum ott124729" Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Fibraurea ott477318" Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Fibraurea ott477318" Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Kolobopetalum ott522768" Novel unsupported node ancestor 0 node(s) before MRCA of "Penianthus ott628586" and "Kolobopetalum ott522768" Novel unsupported node ancestor 0 node(s) before MRCA of "Burasaia ott698917" and "Kolobopetalum ott522768" Novel unsupported node ancestor 0 node(s) before MRCA of "Cucumis rumphianus ott313891" and "Cucumis melo ott1006256" Novel unsupported node ancestor 0 node(s) before MRCA of "Umtiza ott723021" and "Acrocarpus ott1027571" Novel unsupported node ancestor 0 node(s) before MRCA of "Barnebyella ott366943" and "Biserrula ott366947" Confirmation of unsupported node (designators =ott767004 ott3919914) ancestor 0 node(s) before MRCA of "Sophora tonkinensis ott434824" and "Bolusanthus ott807796" Confirmation of unsupported node (designators =ott767001 ott767004) ancestor 0 node(s) before MRCA of "Sophora tonkinensis ott434824" and "Cadia ott434088" Confirmation of unsupported node (designators =ott359842 ott5532343) ancestor 0 node(s) before MRCA of "Baphia ott100710" and "Sophora japonica ott935514" Confirmation of unsupported node (designators =ott3920796 ott5532343) ancestor 0 node(s) before MRCA of "Baphia ott100710" and "Isotropis ott382788" Confirmation of unsupported node (designators =ott935514 ott3920020) ancestor 0 node(s) before MRCA of "Cladrastis parvifolia ott3920020" and "Sophora japonica ott935514" Novel unsupported node ancestor 0 node(s) before MRCA of "Cladrastis parvifolia ott3920020" and "Cladrastis delavayi ott5457" Confirmation of unsupported node (designators =ott799055 ott3919880) ancestor 0 node(s) before MRCA of "Ammodendron ott288771" and "Cadia ott434088" Novel unsupported node ancestor 0 node(s) before MRCA of "Hymenaea ott31275" and "Cynometra ott330639" Novel unsupported node ancestor 0 node(s) before MRCA of "Amherstia ott301507" and "Cynometra ott330639" Novel unsupported node ancestor 0 node(s) before MRCA of "Brachystegia ott65504" and "Cynometra ott330639" Confirmation of unsupported node (designators =ott671286 ott970634) ancestor 0 node(s) before MRCA of "Asterolinon adoense ott671286" and "Asterolinon linum-stellatum ott383202" Confirmation of unsupported node (designators =ott644217 ott671286) ancestor 0 node(s) before MRCA of "Asterolinon adoense ott671286" and "Anagallis monelli ott671287" Novel unsupported node ancestor 0 node(s) before MRCA of "Solanum aviculare ott494825" and "Solanum trisectum ott1026080" Confirmation of unsupported node (designators =ott719936 ott779108) ancestor 0 node(s) before MRCA of "Stenostelma ott779109" and "Margaretta ott728333" Confirmation of unsupported node (designators =ott150151 ott779108) ancestor 0 node(s) before MRCA of "Stenostelma ott779109" and "Asclepias multicaulis ott144808" Novel unsupported node ancestor 0 node(s) before MRCA of "Xysmalobium ott779093" and "Pachycarpus ott119076" Novel unsupported node ancestor 0 node(s) before MRCA of "Eriogonum ott942007" and "Coccoloba ott137596" Novel unsupported node ancestor 0 node(s) before MRCA of "Phaeomegaceros squamuliger ott915124" and "Phaeomegaceros hirticalyx ott639740" Novel unsupported node ancestor 0 node(s) before MRCA of "Hamacanthidae ott2841048" and "Axinella cf polypoides MCP03 144 ott26402" Confirmation of unsupported node (designators =ott2839507 ott2839530) ancestor 0 node(s) before MRCA of "Suberitechnius ott2839508" and "Agelas clathrodes ott163384" Confirmation of unsupported node (designators =ott121609 ott2839091) ancestor 0 node(s) before MRCA of "Polymastiidae ott623032" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304" Confirmation of unsupported node (designators =ott121609 ott2841141) ancestor 0 node(s) before MRCA of "Trachycladidae ott526862" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304" Confirmation of unsupported node (designators =ott2835934 ott2841141) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304" Confirmation of unsupported node (designators =ott2841141 ott2841290) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Merliidae ott2841065" Confirmation of unsupported node (designators =ott2837881 ott2841141) ancestor 0 node(s) before MRCA of "Esperiopsis ott2840905" and "Crambeidae ott644862" Confirmation of unsupported node (designators =ott2837334 ott2837881) ancestor 0 node(s) before MRCA of "Amphilectus ott303949" and "Neopodospongia ott763487" Confirmation of unsupported node (designators =ott2837479 ott2837881) ancestor 0 node(s) before MRCA of "Amphilectus ott303949" and "Isodictya compressa ott2837472" Novel unsupported node ancestor 0 node(s) before MRCA of "Neoesperiopsis ott2837448" and "Isodictya compressa ott2837472" Confirmation of unsupported node (designators =ott2837334 ott2837928) ancestor 0 node(s) before MRCA of "Diacarnus bismarckensis ott2837334" and "Neopodospongia ott763487" Confirmation of unsupported node (designators =ott2837928 ott2837939) ancestor 0 node(s) before MRCA of "Strongylodesma ott2837927" and "Neopodospongia ott763487" Confirmation of unsupported node (designators =ott2838257 ott5440746) ancestor 0 node(s) before MRCA of "Phellodermidae ott206663" and "Crambeidae ott644862" Novel unsupported node ancestor 0 node(s) before MRCA of "Mycale titubans ott403492" and "Hymedesmiidae ott950042" Novel unsupported node ancestor 0 node(s) before MRCA of "Tedaniidae ott962323" and "Hymedesmiidae ott950042" Confirmation of unsupported node (designators =ott2835934 ott5440774) ancestor 0 node(s) before MRCA of "Spongosorites ott641040" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304" Novel unsupported node ancestor 0 node(s) before MRCA of "Tylodesma informis ott5440774" and "Desmacella cf annexa BELUM GBR Mc4240 ott4939304" Confirmation of unsupported node (designators =ott2839648 ott2839660) ancestor 0 node(s) before MRCA of "Sulcastrella ott2839649" and "Axinella cf polypoides MCP03 144 ott26402" Confirmation of unsupported node (designators =ott2835466 ott2835496) ancestor 0 node(s) before MRCA of "Higginsia ott103935" and "Axinella cf polypoides MCP03 144 ott26402" Confirmation of unsupported node (designators =ott2835574 ott2839151) ancestor 0 node(s) before MRCA of "Axinyssa cavernosa ott2835574" and "Sigmaxinella ott917215" Confirmation of unsupported node (designators =ott2839151 ott2840284) ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Sigmaxinella ott917215" Confirmation of unsupported node (designators =ott2839151 ott5448025) ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Hymeraphia ott303945" Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Stelligera ott304841" Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea duplex ott2839151" and "Paratimea sp BELUM GBR Mc6884 ott4938921" Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Paratimea sp BELUM GBR Mc4323 ott4938924" Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Higginsia mixta ott700742" Novel unsupported node ancestor 0 node(s) before MRCA of "Paratimea sp BELUM GBR Mc2937 ott4938926" and "Halicnemia ott776728" Confirmation of unsupported node (designators =ott253718 ott5448025) ancestor 0 node(s) before MRCA of "Raspailia uncinata ott5448025" and "Hymeraphia ott303945" Confirmation of unsupported node (designators =ott5448024 ott5448025) ancestor 0 node(s) before MRCA of "Raspailia uncinata ott5448025" and "Ptilocaulis ott215104" Confirmation of unsupported node (designators =ott303942 ott403483) ancestor 0 node(s) before MRCA of "Raspaciona ott828111" and "Tethyspira ott145572" Confirmation of unsupported node (designators =ott303942 ott644861) ancestor 0 node(s) before MRCA of "Raspaciona ott828111" and "Aulospongus ott417668" Confirmation of unsupported node (designators =ott172864 ott644861) ancestor 0 node(s) before MRCA of "Diacarnus spinipoculum ott644861" and "Aulospongus ott417668" Confirmation of unsupported node (designators =ott644861 ott2841472) ancestor 0 node(s) before MRCA of "Diacarnus spinipoculum ott644861" and "Tetrapocillon ott2840942" Confirmation of unsupported node (designators =ott695752 ott2835288) ancestor 0 node(s) before MRCA of "Raspailia phakellopsis ott695752" and "Ptilocaulis ott215104" Confirmation of unsupported node (designators =ott670457 ott695752) ancestor 0 node(s) before MRCA of "Raspailia phakellopsis ott695752" and "Myrmekioderma granulata ott457665" Confirmation of unsupported node (designators =ott670457 ott2837294) ancestor 0 node(s) before MRCA of "Axechina ott1027061" and "Myrmekioderma granulata ott457665" Confirmation of unsupported node (designators =ott511196 ott2837294) ancestor 0 node(s) before MRCA of "Eurypon hispidum ott2837294" and "Myrmekioderma granulata ott457665" Confirmation of unsupported node (designators =ott2837294 ott2841361) ancestor 0 node(s) before MRCA of "Eurypon hispidum ott2837294" and "Trikentrion ott172860" Novel unsupported node ancestor 0 node(s) before MRCA of "Poicephalus ott225738" and "Psittrichas ott412122" Novel unsupported node ancestor 0 node(s) before MRCA of "Poicephalus ott225738" and "Pionites ott682882" Novel unsupported node ancestor 0 node(s) before MRCA of "Nannopsittaca ott667518" and "Pionites ott682882" Novel unsupported node ancestor 0 node(s) before MRCA of "Mitu ott488150" and "Ortalis ott109892" Novel unsupported node ancestor 0 node(s) before MRCA of "Mitu ott488150" and "Oreophasis ott488144" Confirmation of unsupported node (designators =ott375229 ott3613449) ancestor 0 node(s) before MRCA of "Notopteris ott687489" and "Chironax ott99582" Confirmation of unsupported node (designators =ott3613449 ott3613509) ancestor 0 node(s) before MRCA of "Notopteris ott687489" and "Dobsonia ott988790" Confirmation of unsupported node (designators =ott201393 ott3613509) ancestor 0 node(s) before MRCA of "Epomophorini ott956035" and "Desmalopex ott268705" Confirmation of unsupported node (designators =ott201393 ott3613485) ancestor 0 node(s) before MRCA of "Melonycteris ott687488" and "Desmalopex ott268705" Novel unsupported node ancestor 0 node(s) before MRCA of "Pteropus aruensis ott3613485" and "Desmalopex ott268705" Novel unsupported node ancestor 0 node(s) before MRCA of "Pteropus aruensis ott3613485" and "Pteropus capistratus ott609464" Novel unsupported node ancestor 4 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029" Novel unsupported node ancestor 3 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029" Novel unsupported node ancestor 2 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029" Novel unsupported node ancestor 1 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029" Novel unsupported node ancestor 0 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029" Novel unsupported node ancestor 0 node(s) before MRCA of "Pseudosimochromis ott1089695" and "Limnotilapia ott303029" Novel unsupported node ancestor 0 node(s) before MRCA of "Sphyraenidae ott280947" and "Istiophoriformes ott5554905" Novel unsupported node ancestor 0 node(s) before MRCA of "Cirrhitiformes ott930720" and "Acanthuriformes ott515461" Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Lagocephalus ott986279" Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Chelonodon ott95360" Novel unsupported node ancestor 0 node(s) before MRCA of "Canthigaster ott544462" and "Chonerhinos ott3631233" Confirmation of unsupported node (designators =ott974751 ott3627699) ancestor 0 node(s) before MRCA of "Serpenticobitidae ott5551560" and "Tanichthys ott306827" Confirmation of unsupported node (designators =ott125135 ott3626575) ancestor 0 node(s) before MRCA of "Labeo ott160620" and "Tanichthys ott306827" Novel unsupported node ancestor 0 node(s) before MRCA of "Raiamas ott837023" and "Tanichthys ott306827" Novel unsupported node ancestor 0 node(s) before MRCA of "Leptobarbus ott653127" and "Tanichthys ott306827" Confirmation of unsupported node (designators =ott598619 ott5003672) ancestor 0 node(s) before MRCA of "Dorylaimia ott5424357" and "Isolaimida ott658328" Novel unsupported node ancestor 3 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506" Novel unsupported node ancestor 2 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506" Novel unsupported node ancestor 1 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506" Novel unsupported node ancestor 0 node(s) before MRCA of "Lomoidea ott389510" and "Eumunida ott389506" Confirmation of unsupported node (designators =ott2981100 ott4668275) ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Raninoidea ott233901" Confirmation of unsupported node (designators =ott4668275 ott4668960) ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Corycodus ott38070" Novel unsupported node ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Majoidea ott428460" Novel unsupported node ancestor 0 node(s) before MRCA of "Dorippoidea ott908345" and "Portunoidea ott757096" Novel unsupported node ancestor 1 node(s) before MRCA of "Panopeidae ott938012" and "Portunoidea ott757096" Novel unsupported node ancestor 0 node(s) before MRCA of "Panopeidae ott938012" and "Portunoidea ott757096" Confirmation of unsupported node (designators =ott4667880 ott4668095) ancestor 0 node(s) before MRCA of "Panopeidae ott938012" and "Xanthidae ott757095" Confirmation of unsupported node (designators =ott722710 ott2978847) ancestor 0 node(s) before MRCA of "Eriphiidae ott45361" and "Xanthidae ott757095" Novel unsupported node ancestor 1 node(s) before MRCA of "Dairidae ott531267" and "Carpiliidae ott677778" Confirmation of unsupported node (designators =ott677780 ott722710) ancestor 0 node(s) before MRCA of "Dairidae ott531267" and "Carpiliidae ott677778"

Final summary: 203700 internal nodes were named in the reference tree. These were not rigorously checked against the taxonomy. They may not be detected as errors. 35755 internal nodes where flagged as being supported by an input (including taxonomy). 12477 of these were named (some of the support could just be the taxonomic expansion of tips). 23278 of these were unnamed. 111 unsupported nodes.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72037333 .

No Support: Taxon: Parent_Taxon: FamilyI_ott5247949 -> # Children: 2 Descendant_Leaf: Trichodesmium_sp_7_3B_ott381496 Descendant_Leaf: Lyngbya_wollei_str_Carmichael_Alabama_ott887375 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: _Microcystis_elabens_NIES-42_ott247513 Descendant_Leaf: Oscillatoria_duplisecta_ETS-06_ott301902 No Support: Taxon: Parent_Taxon: -> # Children: 32 Descendant_Leaf: Cyanothece_aeruginosa_I5_ott5258280 Descendant_Leaf: Cyanothece_epiphytica_AUS-JR_DB_NT-021_ott5236290 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Synechococcus_sp_PCC_7335_ott1039386 Descendant_Leaf: Cyanothece_aeruginosa_I5_ott5258280 No Support: Taxon: Parent_Taxon: Cyanobacteria_ott225495 -> # Children: 876 Descendant_Leaf: Synechococcus_rubescens_SAG_3_81_ott1047333 Descendant_Leaf: Synechococcus_nidulans_LMECYA_156_ott826450 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Burasaia_madagascariensis_ott698915 Descendant_Leaf: Borismene_japurensis_ott698911 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Penianthus_patulinervis_ott346197 Descendant_Leaf: Burasaia_madagascariensis_ott698915 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Sphenocentrum_jollyanum_ott576458 Descendant_Leaf: Penianthus_patulinervis_ott346197 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Sphenocentrum_jollyanum_ott576458 Descendant_Leaf: Fibraurea_recisa_ott651522 No Support: Taxon: Parent_Taxon: Fabales_ott956360 -> # Children: 2 Descendant_Leaf: Xanthophyllum_flavescens_ott5515846 Descendant_Leaf: Quillaja_brasiliensis_ott3929907 No Support: Taxon: Parent_Taxon: Galegeae_ott1090347 -> # Children: 2 Descendant_Leaf: Barnebyella_calycina_ott507633 Descendant_Leaf: Biserrula_pelecinus_ott611049 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Baphia_polyantha_ott5532343 Descendant_Leaf: Eutaxia_obovata_ott3920796 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Cladrastis_parvifolia_ott3920020 Descendant_Leaf: Sophora_japonica_ott935514 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Baphia_polyantha_ott5532343 Descendant_Leaf: Pickeringia_montana_var_tomentosa_ott359842 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Ammodendron_karelinii_ott3919880 Descendant_Leaf: Crotalaria_salicifolia_ott799055 No Support: Taxon: Parent_Taxon: -> # Children: 66 Descendant_Leaf: Sophora_tonkinensis_var_polyphylla_ott767004 Descendant_Leaf: Sophora_alopecuroides_var_alopecuroides_ott767001 No Support: Taxon: Parent_Taxon: Papilionoideae_ott39538 -> # Children: 2 Descendant_Leaf: Sophora_tonkinensis_var_polyphylla_ott767004 Descendant_Leaf: Bolusanthus_speciosa_ott3919914 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Brachystegia_mildbraedii_ott200316 Descendant_Leaf: Cynometra_iripa_ott347967 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Amherstia_nobilis_ott301504 Descendant_Leaf: Brachystegia_mildbraedii_ott200316 No Support: Taxon: Parent_Taxon: Detarieae_ott792364 -> # Children: 2 Descendant_Leaf: Hymenaea_altissima_ott5531835 Descendant_Leaf: Amherstia_nobilis_ott301504 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Asterolinon_adoense_ott671286 Descendant_Leaf: Anagallis_arvensis_subsp_arvensis_ott644217 No Support: Taxon: Parent_Taxon: Primulaceae_ott486216 -> # Children: 2 Descendant_Leaf: Asterolinon_adoense_ott671286 Descendant_Leaf: Pelletiera_verna_ott970634 No Support: Taxon: Parent_Taxon: Solanum_ott1020645 -> # Children: 2 Descendant_Leaf: Solanum_aviculare_ott494825 Descendant_Leaf: Solanum_trisectum_ott1026080 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Xysmalobium_parviflorum_ott150151 Descendant_Leaf: Glossostelma_ceciliae_ott234981 No Support: Taxon: Parent_Taxon: -> # Children: 9 Descendant_Leaf: Stenostelma_corniculatum_ott779108 Descendant_Leaf: Xysmalobium_parviflorum_ott150151 No Support: Taxon: Parent_Taxon: Asclepiadeae_ott673333 -> # Children: 2 Descendant_Leaf: Stenostelma_corniculatum_ott779108 Descendant_Leaf: Margaretta_rosea_subsp_corallina_ott719936 No Support: Taxon: Parent_Taxon: Polygonaceae_ott904376 -> # Children: 2 Descendant_Leaf: Eriogonum_cithariforme_ott3943977 Descendant_Leaf: Coccoloba_northropiae_ott452444 No Support: Taxon: Mycale_ott1026107 Parent_Taxon: -> # Children: 263 Descendant_Leaf: Esperia_parasitica_ott5440762 Descendant_Leaf: Esperella_toxifer_ott5440761 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Amphilectus_americanus_ott2837881 Descendant_Leaf: Neoesperiopsis_rigida_ott2837479 No Support: Taxon: Parent_Taxon: -> # Children: 8 Descendant_Leaf: Strongylodesma_tsitsikammaensis_ott2837928 Descendant_Leaf: Cyclacanthia_mzimayiensis_ott2837939 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Diacarnus_bismarckensis_ott2837334 Descendant_Leaf: Strongylodesma_tsitsikammaensis_ott2837928 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Amphilectus_americanus_ott2837881 Descendant_Leaf: Diacarnus_bismarckensis_ott2837334 No Support: Taxon: Parent_Taxon: -> # Children: 9 Descendant_Leaf: Echinostylinos_reticulatus_ott2838257 Descendant_Leaf: Stylotrichophora_arenifibrosa_ott5440746 No Support: Taxon: Parent_Taxon: -> # Children: 3 Descendant_Leaf: Esperiopsis_profunda_ott2841141 Descendant_Leaf: Amphilectus_americanus_ott2837881 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Esperiopsis_profunda_ott2841141 Descendant_Leaf: Merlia_deficiens_ott2841290 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Spongosorites_arenatus_ott2835934 Descendant_Leaf: Tylodesma_informis_ott5440774 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Esperiopsis_profunda_ott2841141 Descendant_Leaf: Spongosorites_arenatus_ott2835934 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Trachycladus_cf_digitatus_G318739_ott121609 Descendant_Leaf: Esperiopsis_profunda_ott2841141 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Acanthopolymastia_acanthotoxa_ott2839091 Descendant_Leaf: Trachycladus_cf_digitatus_G318739_ott121609 No Support: Taxon: Parent_Taxon: -> # Children: 7 Descendant_Leaf: Suberitechnius_hispidus_ott2839507 Descendant_Leaf: Plicatellopsis_flabellata_ott2839530 No Support: Taxon: Higginsia_ott103935 Parent_Taxon: -> # Children: 26 Descendant_Leaf: Higginsia_bidentifera_ott2835466 Descendant_Leaf: Higginsia_higgini_ott2835469 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Diacarnus_spinipoculum_ott644861 Descendant_Leaf: Coelodischela_massa_ott2841472 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Diacarnus_spinipoculum_ott644861 Descendant_Leaf: Ceratopsion_palmata_ott172864 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raspaciona_aculeata_ott303942 Descendant_Leaf: Diacarnus_spinipoculum_ott644861 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raspaciona_aculeata_ott303942 Descendant_Leaf: Eurypon_clavigerum_ott403483 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Eurypon_hispidum_ott2837294 Descendant_Leaf: Cyamon_quinqueradiatum_ott2841361 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Eurypon_hispidum_ott2837294 Descendant_Leaf: Didiscus_oxeata_ott511196 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Axechina_raspailioides_ott670457 Descendant_Leaf: Eurypon_hispidum_ott2837294 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raspailia_phakellopsis_ott695752 Descendant_Leaf: Axechina_raspailioides_ott670457 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raspailia_phakellopsis_ott695752 Descendant_Leaf: Ptilocaulis_aulopora_ott2835288 No Support: Taxon: Parent_Taxon: -> # Children: 147 Descendant_Leaf: Raspailia_uncinata_ott5448025 Descendant_Leaf: Raspailia_simplicior_ott5448024 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raspailia_uncinata_ott5448025 Descendant_Leaf: Hymeraphia_breeni_ott253718 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Paratimea_duplex_ott2839151 Descendant_Leaf: Raspailia_uncinata_ott5448025 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Paratimea_duplex_ott2839151 Descendant_Leaf: Amphitethya_microsigma_ott2840284 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Axinyssa_cavernosa_ott2835574 Descendant_Leaf: Paratimea_duplex_ott2839151 No Support: Taxon: Parent_Taxon: -> # Children: 13 Descendant_Leaf: Higginsia_bidentifera_ott2835466 Descendant_Leaf: Myrmekioderma_tuberculatum_ott2835496 No Support: Taxon: Parent_Taxon: -> # Children: 107 Descendant_Leaf: Sulcastrella_leviorum_ott2839648 Descendant_Leaf: Paradesmanthus_macphersoni_ott2839660 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Anhinga_subvolans_ott3600642 Descendant_Leaf: Phalacrocorax_olivaceus_ott5560119 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Caprimulgus_arizonae_ott3597078 Descendant_Leaf: Eurostopodus_argus_ott847125 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Mitu_mitu_x_Mitu_tuberosa_ott4947475 Descendant_Leaf: Oreophasis_derbianus_ott488145 No Support: Taxon: Parent_Taxon: Cracidae_ott109893 -> # Children: 2 Descendant_Leaf: Mitu_mitu_x_Mitu_tuberosa_ott4947475 Descendant_Leaf: Ortalis_cinereiceps_ott520559 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Pteropus_aruensis_ott3613485 Descendant_Leaf: Desmalopex_leucopterus_ott740197 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Melonycteris_fardoulisi_mengermani_ott201393 Descendant_Leaf: Pteropus_aruensis_ott3613485 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Epomops_dobsonii_ott3613509 Descendant_Leaf: Melonycteris_fardoulisi_mengermani_ott201393 No Support: Taxon: Parent_Taxon: -> # Children: 3 Descendant_Leaf: Notopteris_neocaledonica_ott3613449 Descendant_Leaf: Epomops_dobsonii_ott3613509 No Support: Taxon: Parent_Taxon: Chiroptera_ott574724 -> # Children: 2 Descendant_Leaf: Notopteris_neocaledonica_ott3613449 Descendant_Leaf: Megaerops_kusnotoi_ott375229 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Pseudosimochromis_curvifrons_ott1089678 Descendant_Leaf: Limnotilapia_dardennii_ott303030 No Support: Taxon: Parent_Taxon: Carangimorphariae_ott5553751 -> # Children: 2 Descendant_Leaf: Sphyraena_helleri_ott691690 Descendant_Leaf: Xiphias_gladius_ott358621 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Canthigaster_figueiredoi_ott3631131 Descendant_Leaf: Monotrete_cochinchinensis_ott479673 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Canthigaster_figueiredoi_ott3631131 Descendant_Leaf: Chelonodon_pleurospilus_ott479641 No Support: Taxon: Parent_Taxon: Tetraodontidae_ott65336 -> # Children: 2 Descendant_Leaf: Canthigaster_figueiredoi_ott3631131 Descendant_Leaf: Lagocephalus_exilis_ott5560884 No Support: Taxon: Parent_Taxon: Percomorpharia_ott5553753 -> # Children: 2 Descendant_Leaf: Aplodactylus_guttatus_ott3635274 Descendant_Leaf: Scolopsis_margaritifera_ott461423 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Leptobarbus_hosii_ott521734 Descendant_Leaf: Gobiobotia_nicholsi_ott3626725 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Raiamas_salmolucius_ott125135 Descendant_Leaf: Leptobarbus_hosii_ott521734 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Labeo_macrostoma_ott3626575 Descendant_Leaf: Raiamas_salmolucius_ott125135 No Support: Taxon: Parent_Taxon: Cypriniformes_ott1005931 -> # Children: 4 Descendant_Leaf: Serpenticobitis_cingulata_ott3627699 Descendant_Leaf: Barbucca_diabolica_ott974751 No Support: Taxon: Parent_Taxon: Nematoda_ott395057 -> # Children: 2 Descendant_Leaf: Hystrichis_acanthocephalicus_ott5003672 Descendant_Leaf: Isolaimium_sp_2-PM-2004_ott598619 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Daira_americana_ott722710 Descendant_Leaf: Carpilius_convexus_ott677780 No Support: Taxon: Parent_Taxon: -> # Children: 1 Descendant_Leaf: Daira_americana_ott722710 Descendant_Leaf: Carpilius_convexus_ott677780 No Support: Taxon: Parent_Taxon: -> # Children: 3 Descendant_Leaf: Eriphia_smithii_ott2978847 Descendant_Leaf: Daira_americana_ott722710 No Support: Taxon: Parent_Taxon: -> # Children: 9 Descendant_Leaf: Odontoplax_chacei_ott4668095 Descendant_Leaf: Hephthopelta_apta_ott4667880 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Odontoplax_chacei_ott4668095 Descendant_Leaf: Enoplolambrus_carinatus_ott2979557 No Support: Taxon: Parent_Taxon: -> # Children: 1 Descendant_Leaf: Odontoplax_chacei_ott4668095 Descendant_Leaf: Enoplolambrus_carinatus_ott2979557 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Parethusa_hylophora_ott4668275 Descendant_Leaf: Odontoplax_chacei_ott4668095 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Parethusa_hylophora_ott4668275 Descendant_Leaf: Criocarcinus_superciliosus_ott4667135 No Support: Taxon: Parent_Taxon: -> # Children: 2 Descendant_Leaf: Parethusa_hylophora_ott4668275 Descendant_Leaf: Cyclodorippe_angulata_ott4668960 No Support: Taxon: Parent_Taxon: Brachyura_ott935379 -> # Children: 2 Descendant_Leaf: Parethusa_hylophora_ott4668275 Descendant_Leaf: Symethis_garthi_ott2981100

Some pairs of designators appear multiple times because they are referring to nodes with out degree = 1. See https://devtree.opentreeoflife.org/opentree/otol.draft.22@3856216/Simochromis that is the node that my code refers to as "4 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"'

Its daughter is the "3 node(s) before ...

The synthetic tree which I received from Joseph had a lot of special characters. My C/C++ program couldn't run on that file without deleting all of them. Did you also do the same? I just uploaded a synthetic tree file ("OpenTree1.tre") and taxonomy file ("Taxonomy1.tre") in our shared folder. Can you please run your method on these files? I am curious!

On Thu, Jan 29, 2015 at 12:32 PM, Mark T. Holder notifications@github.com wrote:

Some pairs of designators appear multiple times because they are referring to nodes with out degree = 1. See https://devtree.opentreeoflife.org/opentree/otol.draft.22@3856216/Simochromis that is the node that my code refers to as "4 node(s) before MRCA of "Simochromis ott710023" and "Limnotilapia ott303029"'

Its daughter is the "3 node(s) before ...

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72077953 .

just ran it again @ruchiherself . It only changed a taxon label in the first line error report. no other differences from using the other files. thanks.

I checked first 5 "Novel" nodes. Results are as follows:

1) Novel unsupported node ancestor 0 node(s) before MRCA of "Trichodesmium ott196997" and "Lyngbya ott878838" It is included in the list of 87 nodes. (It wasn't there in the 56 nodes.)

2) Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Calycocarpum ott124729" This is root node ("cellular_organisms_ott93302"), so irrelevant with respect to each input tree.

3) Novel unsupported node ancestor 0 node(s) before MRCA of "Disciphania ott550889" and "Fibraurea ott477318" This node gets 1 support, 1 conflict, and 1 permit from input trees. Tree "pg_2644_6164.tre" supports it.

4) Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Fibraurea ott477318" This is again the root of synthetic tree.

5) Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Kolobopetalum ott522768" This node is labeled "bacterium_enrichment_culture_clone_R4-85B_ott5183791". It looks like it has only one leaf under it. I need to investigate more on this.

On Thu, Jan 29, 2015 at 1:46 PM, Mark T. Holder notifications@github.com wrote:

just ran it again @ruchiherself https://github.com/ruchiherself . It only changed a taxon label in the first line error report. no other differences from using the other files. thanks.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72091080 .

I don't understand why my software is claiming the MRCA "Disciphania ott550889" and "Fibraurea ott477318" is a problem. I'll look into that. Thanks.

The MRCA for cases 2 is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840209 for case 4 it is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840206 Neither is the root of the tree.

I'll start a new issue for the problem that my software is trying to detect. It its not the same as definition of unsupported as the conflict definition from Wilkinson. So it seems wise to clarify the discussion by keeping this thread about the problems that your software detects, and create a new issue on the unsupported definition that my software uses.

The MRCA for case 2 & 4 is the root of the synthetic tree. It has 2339460 leaves under, that's the total number of leaves in the synthetic tree. Does the newick string which I shared with you shows it's not a root?

Case 5: Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Kolobopetalum ott522768" This node is labeled "bacterium_enrichment_culture_clone_R4-85B_ott5183791" and it has only one leaf under it, so irrelevent. I found that "Sphenocentrum ott576456" and "Kolobopetalum ott522768" are not leaves in the synthetic tree. Both are degree two nodes. Here is the substring of synthetic tree's newick string, and you can see

"Sphenocentrum ott576456" labels internal node.

,(((Sphenocentrum_jollyanum_ott576458)Sphenocentrum_ott576456,((Penianthus_patulinervis_ott346197,Penianthus

On Fri, Jan 30, 2015 at 3:03 AM, Mark T. Holder notifications@github.com wrote:

I don't understand why my software is claiming the MRCA "Disciphania ott550889" and "Fibraurea ott477318" is a problem. I'll look into that. Thanks.

The MRCA for cases 2 is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840209 for case 4 it is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840206 Neither is the root of the tree.

I'll start a new issue for the problem that my software is trying to detect. It its not the same as definition of unsupported as the conflict definition from Wilkinson. So it seems wise to clarify the discussion by keeping this thread about the problems that your software detects, and create a new issue on the unsupported definition that my software uses.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72172473 .

6) Novel unsupported node ancestor 0 node(s) before MRCA of "Penianthus ott628586" and "Kolobopetalum ott522768" This is root node, it has 2339460 leaves under it.

7) Novel unsupported node ancestor 0 node(s) before MRCA of "Burasaia ott698917" and "Kolobopetalum ott522768" Root node again.

8) Novel unsupported node ancestor 0 node(s) before MRCA of "Cucumis rumphianus ott313891" and "Cucumis melo ott1006256" This node is supported by 2 input trees, one of them is taxonomy.

9) Novel unsupported node ancestor 0 node(s) before MRCA of "Umtiza ott723021" and "Acrocarpus ott1027571" Root node again.

10) Novel unsupported node ancestor 0 node(s) before MRCA of "Barnebyella ott366943" and "Biserrula ott366947" Root node again. 11) Novel unsupported node ancestor 0 node(s) before MRCA of "Cladrastis parvifolia ott3920020" and "Cladrastis delavayi ott5457" This node gets 1 support and 1 conflict. Taxonomy supports it.

I will stop here, and wait for Mark's input.

On Fri, Jan 30, 2015 at 10:12 AM, Ruchi ruchiherself@gmail.com wrote:

The MRCA for case 2 & 4 is the root of the synthetic tree. It has 2339460 leaves under, that's the total number of leaves in the synthetic tree. Does the newick string which I shared with you shows it's not a root?

Case 5: Novel unsupported node ancestor 0 node(s) before MRCA of "Sphenocentrum ott576456" and "Kolobopetalum ott522768" This node is labeled "bacterium_enrichment_culture_clone_R4-85B_ott5183791" and it has only one leaf under it, so irrelevent. I found that "Sphenocentrum ott576456" and "Kolobopetalum ott522768" are not leaves in the synthetic tree. Both are degree two nodes. Here is the substring of synthetic tree's newick string, and you can see

"Sphenocentrum ott576456" labels internal node.

,(((Sphenocentrum_jollyanum_ott576458)Sphenocentrum_ott576456,((Penianthus_patulinervis_ott346197,Penianthus

On Fri, Jan 30, 2015 at 3:03 AM, Mark T. Holder notifications@github.com wrote:

I don't understand why my software is claiming the MRCA "Disciphania ott550889" and "Fibraurea ott477318" is a problem. I'll look into that. Thanks.

The MRCA for cases 2 is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840209 for case 4 it is https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840206 Neither is the root of the tree.

I'll start a new issue for the problem that my software is trying to detect. It its not the same as definition of unsupported as the conflict definition from Wilkinson. So it seems wise to clarify the discussion by keeping this thread about the problems that your software detects, and create a new issue on the unsupported definition that my software uses.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72172473 .

Hi @ruchiherself case 2 is the MRCA of "Disciphania ott550889" and "Calycocarpum ott124729" both of those are plants. In fact you can see them on the same screen at https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840209 They do not span the root in the newick that you sent me. It is hard for me to trim out the relevant portion. but you can search for one in vim and see the other not far away.

My code skips the root of the tree. So unless the tree has a root of out-degree 1, the root is not reported.

On the other thread for https://github.com/OpenTreeOfLife/treemachine/issues/156 I posted a link http://phylo.bio.ku.edu/ot/findunsupportededges-out.txt which is the same groups. but does not use and higher taxonomic names in the mrca designators. that may be easier for you to work with that list.

My code had some difficulty in finding the right MRCA for internal nodes; providing leaf nodes (at http://phylo.bio.ku.edu/ot/findunsupportededges-out.txt) was great help. I looked at cases 2,3, and 4 again.

2) Novel unsupported node MRCA of "Disciphania lobata ott477320" and "Calycocarpum lyonii ott124731" It gets 1 support, 1 permit, and 1 conflict (rest irrelevant). It's supported by pg_2644_6164.tre

3) Novel unsupported node MRCA of "Disciphania lobata ott477320" and "Fibraurea chloroleuca ott446599" It gets 1 support, 1 permit, and 1 conflict. It's supported by pg_2644_6164.tre

4) Novel unsupported node MRCA of "Sphenocentrum jollyanum ott576458" and "Fibraurea chloroleuca ott446599" It gets 0 support, 1 permit, and 1 conflict. It's already in my list.

Mark, I can check remaining "Novel" nodes, if these three make sense now.

On Fri, Jan 30, 2015 at 11:33 AM, Mark T. Holder notifications@github.com wrote:

Hi @ruchiherself https://github.com/ruchiherself case 2 is the MRCA of "Disciphania ott550889" and "Calycocarpum ott124729" both of those are plants. In fact you can see them on the same screen at https://tree.opentreeoflife.org/opentree/argus/otol.draft.22@3840209 They do not span the root in the newick that you sent me. It is hard for me to trim out the relevant portion. but you can search for one in vim and see the other not far away.

My code skips the root of the tree. So unless the tree has a root of out-degree 1, the root is not reported.

On the other thread for #156 https://github.com/OpenTreeOfLife/treemachine/issues/156 I posted a link http://phylo.bio.ku.edu/ot/findunsupportededges-out.txt which is the same groups. but does not use and higher taxonomic names in the mrca designators. that may be easier for you to work with that list.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/treemachine/issues/78#issuecomment-72238423 .

Note that I addressed why my code considers case 2 to be unsupported. Quoting from https://github.com/OpenTreeOfLife/treemachine/issues/156 :

"This difference in evaluation explains why my software classifies this group to be unsupported, while Ruchi's code considers pg_2644_6164.tre to support it. The source tree does indeed have a grouping of (Aspidocarya + Parabaena) + (Tinomiscium + Tinospora). But if we back up one node in the synthetic tree, we see that the sister group is Calycocarpum. Calycocarpum is not sampled in pg_2644_6164.tre. So, according to that source tree there is no reason that you could not have any resolution of the 3 way polytomy: (Calycocarpum, (Aspidocarya, Parabaena), (Tinomiscium, Tinospora))"

(comment moved here, had been wrongly added to #156) I can't pretend to understand this very well, but here's what I've got so far. I found a different, although perhaps equivalent definition of support in http://www.lirmm.fr/~vberry/Publis/RR07010.pdf : a set R of rooted triples, say from input trees, supports (or 'induces') another set S of rooted triples, e.g. S equivalent to an ingroup/outgroup pair, if there is a subset of R that entails (displays / necessitates) S. If I understand what Cody has told me recently about testSum, it is this definition of support that is implemented (perhaps conservatively) by testSum. And if I read the methods supplement correctly, no support check is made when adding 'accumulation nodes' to the TAG, unlike merger nodes, which do get a support check. So, if the methods supplement correctly describes what the code does, any unsupported nodes must be accumulation nodes that would fail the testSum check, were it to be performed.

OpenTreeOfLife / treemachine