Tree-average distances on certain phylogenetic networks have their weights uniquely determined 英文参考文献.docVIP

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Tree-average distances on certain phylogenetic networks have their weights uniquely determined 英文参考文献.doc

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Tree-average distances on certain phylogenetic networks have their weights uniquely determined 英文参考文献

WillsonAlgorithmsforMolecularBiology2012,7:13 /content/7/1/13 RESEARCH OpenAccess Tree-averagedistancesoncertainphylogenetic networkshavetheirweightsuniquelydetermined StephenJWillson Abstract AphylogeneticnetworkNhasverticescorrespondingtospeciesandarcscorrespondingtodirectgenetic inheritancefromthespeciesatthetailtothespeciesatthehead.MeasurementsofDNAareoftenmadeon speciesintheleafset,andoneseekstoinferpropertiesofthenetwork,possiblyincludingthegraphitself.Inthe caseofphylogenetictrees,distancesbetweenextantspeciesarefrequentlyusedtoinferthephylogenetictreesby methodssuchasneighbor-joining. Thispaperproposesatree-averagedistancefornetworksmoregeneralthantrees.Thenotionrequiresaweighton eacharcmeasuringthegeneticchangealongthearc.Foreachdisplayedtreethedistancebetweentwoleavesis thesumoftheweightsalongthepathjoiningthem.Atahybridvertex,eachcharacterisinheritedfromoneofits parents.Wewillassumethatforeachhybridthereisaprobabilitythattheinheritanceofacharacterisfroma specifiedparent.Assumethattheinheritanceeventsatdifferenthybridsareindependent.Thenforeachdisplayed treetherewillbeaprobabilitythattheinheritanceofagivencharacterfollowsthetree;thisprobabilitymaybe interpretedastheprobabilityofthetree.Thetree-averagedistancebetweentheleavesisdefinedtobethe expectedvalueoftheirdistanceinthedisplayedtrees. Foraclassofrootednetworksthatincludesrootedtrees,itisshownthattheweightsandtheprobabilitiesateach hybridvertexcanbecalculatedgiventhenetworkandthetree-averagedistancesbetweentheleaves.Hence theseweightsandprobabilitiesareuniquelydetermined.Thehypothesesonthenetworksincludethathybrid verticeshaveindegreeexactly2andthatverticesthatarenotleaveshaveatree-child. Keywords:digraph,distance,metric,hybrid,network,tree-child,normalnetwork,phylogeny 1Introduction maximum parsimony, maximum likelihood, and Baye- Inphylogeny, theevolution ofacollection ofspecies is sian. See[6] foranoverview. Thesemethods, however, modelledviaadirected graphinwhichthevertices are areonlyhe