NHX format including losses?

[Jolien van Hooff]

Dear Benoit,

I have been exploring the reconciliation results from my single gene trees. I saw that the XML format is richter, since it also contains the losses (such as <loss speciesLocation="Plasmodiophoridae"/>). This information in currently not in the NHX format, while Notung has suggestions to include this (such as with 'Eutheria*LOST[&&NHX:S=Eutheria]').

Moreover, I observed that the spots at which the loss events are placed in the XML differ from the ones in the '_speciesEventCounts.txt' file; in the latter the loss events are in the parent node compared to the XML. Is there a reason for that?

Thanks in advance!

Jolien van Hooff

[Benoit Morel]

Dear Jolien,

Regarding losses in NHX: I don't have the time to work on it right now, but I created an issue here https://github.com/BenoitMorel/GeneRax/issues/48.

Could you please provide an example NHX file with losses that I can open with Notung?

Regarding the loss position in speciesEventCounts.txt file: the value represents the number of speciation-loss (SL) events, that is, a speciation that survives on one lineage and goes extinct on the other lineage. So the SL event is placed in the parent of the node under which the exctinction happens. It seemed to make sense to me when I wrote it, but now I think I should have counted loss events instead (because you can't know from this file on which of the two lineages the loss occurs).

I will think about changing the content of this file...

Can you confirm that this explanation makes sense on your examples?

Best,

Benoit

[Jolien van Hooff]

Dear Benoit,

Thanks for your reply! For me it's not urgent, I am creating a workaround by parsing the XML. I here below you find such a Notung product containing losses

Yes, your rationale and explanation of the way the loss events are reported in speciesEventCounts.txt is clear. Good to be aware of it.

Best wishes,

Jolien

filename: OG0004453_anc.1.pruned.newick.rearrange.0

((((((((((BigNatCCMP2755021204_OG0004453:0.02118[&&NHX:S=BigNatCCMP2755],BigLonCCMP242003667_OG0004453:0.03986[&&NHX:S=BigLonCCMP242])n14:0.14651[&&NHX:S=Bigelowiella:D=N:B=0.88],NorSphBC52*LOST[&&NHX:S=NorSphBC52])r202[&&NHX:S=Chlorarachniophyceae1],ChlRep*LOST[&&NHX:S=ChlRep])r203[&&NHX:S=Chlorarachniophyceae2],(((Gym_CCMP2014012076_OG0004453:0.21856[&&NHX:S=Gym_CCMP2014],LotAmoCCMP2058*LOST[&&NHX:S=LotAmoCCMP2058])r200[&&NHX:S=Chlorarachniophyceae3],ParGloRCC365*LOST[&&NHX:S=ParGloRCC365])r201[&&NHX:S=Chlorarachniophyceae4],(Lot_CCMP622006200_OG0004453:0.11337[&&NHX:S=Lot_CCMP622],LotGloLEX01012472_OG0004453:5.8E-4[&&NHX:S=LotGloLEX01])r103[&&NHX:S=Lotharella:D=N])r98[&&NHX:S=Chlorarachniophyceae5:D=N])n20:0.12073[&&NHX:S=Reticulofilosa:D=N:B=0.837],(((NorSphBC52013902_OG0004453:0.16065[&&NHX:S=NorSphBC52],Bigelowiella*LOST[&&NHX:S=Bigelowiella])r204[&&NHX:S=Chlorarachniophyceae1],ChlRep014276_OG0004453:0.18339[&&NHX:S=ChlRep])r84[&&NHX:S=Chlorarachniophyceae2:D=N],((((LotAmoCCMP2058012559_OG0004453:0.0[&&NHX:S=LotAmoCCMP2058],LotAmoCCMP2058011853_OG0004453:0.0[&&NHX:S=LotAmoCCMP2058])n9:0.32351[&&NHX:S=LotAmoCCMP2058:D=Y:B=1.0],Gym_CCMP2014*LOST[&&NHX:S=Gym_CCMP2014])r205[&&NHX:S=Chlorarachniophyceae3],ParGloRCC365*LOST[&&NHX:S=ParGloRCC365])r206[&&NHX:S=Chlorarachniophyceae4],Lotharella*LOST[&&NHX:S=Lotharella])r207[&&NHX:S=Chlorarachniophyceae5])r83[&&NHX:S=Reticulofilosa:D=N])n23:0.1344[&&NHX:S=Reticulofilosa:D=Y:B=0.952],(((ParGloRCC365006387_OG0004453:5.6E-4[&&NHX:S=ParGloRCC365],Chlorarachniophyceae3*LOST[&&NHX:S=Chlorarachniophyceae3])r208[&&NHX:S=Chlorarachniophyceae4],Lotharella*LOST[&&NHX:S=Lotharella])r209[&&NHX:S=Chlorarachniophyceae5],Chlorarachniophyceae2*LOST[&&NHX:S=Chlorarachniophyceae2])r210[&&NHX:S=Reticulofilosa])n25:0.38285[&&NHX:S=Reticulofilosa:D=Y:B=0.971],((((MatSpe017603_OG0004453:0.58556[&&NHX:S=MatSpe],AboPro*LOST[&&NHX:S=AboPro])r211[&&NHX:S=Monadofilosa3],Silicofilosea*LOST[&&NHX:S=Silicofilosea])r212[&&NHX:S=Monadofilosa2],Monadofilosa4*LOST[&&NHX:S=Monadofilosa4])r213[&&NHX:S=Monadofilosa1],GutVulBF0784*LOST[&&NHX:S=GutVulBF0784])r214[&&NHX:S=Monadofilosa])r69[&&NHX:S=Cercozoa1:D=N],((LapGus005961_OG0004453:0.30831[&&NHX:S=LapGus],Endomyxa2*LOST[&&NHX:S=Endomyxa2])r215[&&NHX:S=Endomyxa1],MikMac*LOST[&&NHX:S=MikMac])r216[&&NHX:S=Endomyxa])n29:0.05199[&&NHX:S=Cercozoa:D=N:B=0.824],((((((RosSpe008875_OG0004453:0.3103[&&NHX:S=RosSpe],(ElpMar001430_OG0004453:0.32113[&&NHX:S=ElpMar],AmmSpe*LOST[&&NHX:S=AmmSpe])r217[&&NHX:S=Rotaliidas2])n5:1.05282[&&NHX:S=Rotaliidas1:D=N:B=0.903],GloSpeGF15*LOST[&&NHX:S=GloSpeGF15])r218[&&NHX:S=Rotaliidas],(SorSpe018094_OG0004453:0.0[&&NHX:S=SorSpe],SorSpe010314_OG0004453:0.0[&&NHX:S=SorSpe])n2:1.54642[&&NHX:S=SorSpe:D=Y:B=1.0])r62[&&NHX:S=Retaria3:D=N],RetFil*LOST[&&NHX:S=RetFil])r219[&&NHX:S=Retaria2],StiZan*LOST[&&NHX:S=StiZan])r220[&&NHX:S=Retaria1],LitSet*LOST[&&NHX:S=LitSet])r221[&&NHX:S=Retaria])n30:0.15597[&&NHX:S=Rhizaria:D=N:B=0.853],(((((((PauChr010232_OG0004453:0.21503[&&NHX:S=PauChr],EugRot*LOST[&&NHX:S=EugRot])r222[&&NHX:S=Silicofilosea],Monadofilosa3*LOST[&&NHX:S=Monadofilosa3])r223[&&NHX:S=Monadofilosa2],Monadofilosa4*LOST[&&NHX:S=Monadofilosa4])r224[&&NHX:S=Monadofilosa1],GutVulBF0784*LOST[&&NHX:S=GutVulBF0784])r225[&&NHX:S=Monadofilosa],Reticulofilosa*LOST[&&NHX:S=Reticulofilosa])r226[&&NHX:S=Cercozoa1],((((LepVor028677_OG0004453:9.9E-4[&&NHX:S=LepVor],Plasmodiophoridae*LOST[&&NHX:S=Plasmodiophoridae])r227[&&NHX:S=Endomyxa3],GroSph*LOST[&&NHX:S=GroSph])r228[&&NHX:S=Endomyxa2],LapGus*LOST[&&NHX:S=LapGus])r229[&&NHX:S=Endomyxa1],MikMac*LOST[&&NHX:S=MikMac])r230[&&NHX:S=Endomyxa])r38[&&NHX:S=Cercozoa:D=N],Retaria*LOST[&&NHX:S=Retaria])r231[&&NHX:S=Rhizaria])n34[&&NHX:S=Rhizaria:D=Y];