Hi everyone, I have a set of gene trees (resulting from RAxML) analyses that I would like to manipulate before inputting them into a coalescence analysis.
I have unrooted trees with bootstrap support as node labels. I would need to collapse branches with less than 50%BS, and root these trees. I'm using a combination of packages (ape, phytools, phangorn) to achieve these results. When visualizing the trees (using ggtree), I noticed that the order of the steps makes a difference in the final output tree. See attached script, dataset and tree comparison PDF. For example (in PDF), if I collapse branches first, then root the tree, I get tree # 3. But, if I do the rooting first, then collapsing branches, I get tree # 4, as well as warnings that "number of items to replace is not a multiple of replacement length" in some steps. Tree #1 is the original tree, unrooted, uncollapsed, straight from RAxML. Tree # 2 is the collapsed, but unrooted tree. The differences in topology are so striking that they influence (a lot!) the final topology and support of the coalescence analysis. I've read before that different software plots/uses the support-as-node-label in different ways, and that could create erroneous representations. But, I can't seem to understand which one is the correct one in my case. Any thoughts on what could be happening here? what would be the order in which the steps should be performed? or any recommendations for different packages to use that could solve the issue? Monica. Monica Carlsen, PhD - Plant systematics, ecology and evolution Peter Buck Postdoctoral Fellow | Smithsonian National Museum of Natural History | Washington, D.C. Research Associate | Missouri Botanical Garden | St. Louis, MO
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(Alpinia-nigra_S81:0.03184297887226069518,(((Amomum-tsaoko_S136:0.01796410930062398645,Hornstedtia-bella_S144:0.01683757952996423751)23:0.00062279298075639119,(Alpinia-oblongifolia_S125:0.01528637716800763761,Siliqamomum-tonkinense_S56:0.01041410179831749570)45:0.00214778769381713608)41:0.00213489627333789730,((((Hedychium-ellipticum_S245:0.04867051910498942924,(Monolophus-appendiculatus_S289:0.04649254011854245944,Zingiber-citriodorum_S171:0.04869818931034498866)60:0.00579007477890952811)54:0.00627981201313514235,(Curcuma-flaviflora_S315:0.02339195928846411407,Globba-marantina_S33:0.03570832958427672121)19:0.00453605108412257971)55:0.00962088594619393139,((((((Strelitzia-nicolai_S351:0.04686591539418533126,Phenakospermum-guyanense_S142:0.03231026778251772091)100:0.03943313165758823707,((Phoenix-dactylifera_cds:0.36670890922124710354,((((Siphonochilus-decorus_S24:0.03828777274686123722,Siphonochilus-aethiopicus_S130:0.04600089956779033346)100:0.24905227835596741026,Orchidantha-chinensis_S352:0.09644336529321007045)89:0.04172604773291348212,(Musa-acuminata_cds:0.15564517594632126807,Musa-balbisiana_cds:0.16160157737268104894)98:0.08063641971393820107)66:0.02035845044801045528,Hanguana-malayana_S373:0.29831138746093122105)53:0.01912360108374845311)99:0.06325810617215976706,(Heliconia-waoraniana_S350:0.02157465452422289987,((Heliconia-lingulata_S348:0.03903072441094616873,Heliconia-pastazae_S349:0.02924543610075551470)44:0.01068522774459718973,(Heliconia-bourgaeana_S347:0.01638288866073665459,(Heliconia-aurantiaca_S345:0.02744177782588659922,Heliconia-bihai_S346:0.01481652307150031593)80:0.01033768433399129619)88:0.01414177470340003025)34:0.00649178195383693767)69:0.01705419353590357720)87:0.02579361881708988266)63:0.02176696237170615625,((Ensete-superbum_S375:0.06645976804580160102,Musella-lasiocarpa_S132:0.03520784263334508085)100:0.07472307885734986999,Ravenala-madagascariensis_S181:0.08556400458165706879)49:0.01498395414425369478)100:0.04384621065533889084,(Canna-liliiflora_S402:0.10875784870745550115,((Calathea-crotalifera_S401:0.09343894828696670818,(Phrynium-imbricatum_S133:0.02838496563824766811,Stachyphrynium-sinense_S377:0.05757985697900207256)100:0.06593393972159240779)94:0.03746593470477422444,Sarcophrynium-sweinfurthianum_S353:0.12558246305038764379)100:0.05255605924490775599)39:0.01224889275851140553)67:0.01767884593339646634,(Paracostus-paradoxus_S266:0.05686979523489998217,(((Monocostus-uniflorus_S187:0.04642925136379201512,Dimerocostus-argenteus_S190:0.04889325853037668201)87:0.02208802606629343621,(Costus-curvibracteatus_S246:0.03740361019347731436,Costus-talbotii_S189:0.04094282489611274223)66:0.01552737534481502500)67:0.02204386990371855551,(((Costus-tonkinensis_S268:0.04411644961786208297,Tapeinochilos-ananassae_S182:0.04004267117852004787)62:0.02009024715122170388,((Costus-afer_S185:0.02844067408409236761,Costus-spectabilis_S269:0.04773493304310575530)59:0.01861207671065135197,(Costus-phaeotrichus_S306:0.04105531151259314560,Costus-scaber_S305:0.03433935584706794553)99:0.04154091471342107045)21:0.01324233626045753440)10:0.00688365693905173409,Chamaecostus-cuspidatus_S191:0.09489406684857062957)31:0.00887013993307724652)47:0.00741522420130059923)100:0.06910443959457610030)100:0.15062853543142173951,Tamijia-flagellaris_S22:0.07662394112143736113)62:0.01985508289005897750)95:0.01376905791942593243,Renealmia-polypus_S66:0.02868289163106648235)62:0.00271315073657741332)29:0.00135414000097462206,Pleuranthodium-racemigerum_S135:0.02673670806086932833);
Rplot11.pdf
Description: Adobe PDF document
TreeComparisons.R
Description: Binary data
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