Phylogenetic Signal with Induction and non-Contradiction - V Berry

Phy logenetic S ignal with I nduction and non- C ontradiction: the PhySIC method for building supertrees http:/atgc.lirmm.fr/SuperTree/PhySIC Vincent Berry 1 , V. Ranwez 2 , A. Criscuolo 1,2 , P.-H. Fabre 2 , S. Guillemot 1 , C. Scornavacca 1,2 , E.J.P. Douzery 2 Funded by ACI IMPBIO & BIOSTIC LR 1 2

Introduction: use of supertrees ,[object Object],[object Object],[object Object],[object Object],[object Object]

Introduction : dealing with conflicts ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],D C B A C B D A

Veto methods ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Axiomatic approach: important properties Reliable facts are those that can be induced from testimonies and that are not incompatible with any other. The superTree method The inspector Phylogenetic information contained within source trees The testimonies The source trees The witnesses SuperTree Police investigation Deducing new facts by cross-checking Pointing out contradictions in the testimonies Deducing the true story

Decomposition of trees in building stones T 1 T 2 ac|d Triplets (rooted triples): subtrees on 3 taxa d c b a c d b e d c a d b a tr(T 1 ) d c b c b a bc|d ac|d ab|d ab|c ed|c eb|d eb|c tr(T 2 ) bd|c

Properties of interest: identification ,[object Object],[object Object],[object Object],bc|d ab|c T d c b a c b a d c b ab|c ab|d R’ does not identify T R identifies T ,[object Object],[object Object],[object Object],c d b a X

[object Object],[object Object],[object Object],Properties of interest: identification d c b bc|d ab|c c b a R d ab|d and ac|d are induced T c b a

[object Object],[object Object],Relevant properties: induction (PI) we only accept supertrees T such that tr(T) is present in the data R or induced by hypotheses in R PI d c b a ab|c ab|d ac|d? cd|b? c b a d b a R d c b a ab|c ab|d ac|d? bc|d? d c b a ab|c ab|d

Focusing on a coherent subset of hypotheses ,[object Object],[object Object],[object Object],find a subset R’ of R identifying a tree (ie, a subtree of the underlying tree) ,[object Object],R ab|c bc|d ab|d ac|d ad|c bd|c d c b a c d b a Supertree method ? R identifies T T

Relevant properties: non-contradiction ,[object Object],[object Object],we reject subsets R’ obtained by keeping xy|z and removing xz|y. ab|c ab|d bc|d ac|d bd|c ad|c R’  R We focus on R(T) , the triplets of R resolved by T we don’t accept hypotheses that are in direct contradiction with discarded hypotheses dc b a T R’ identifies T PC

Link between the properties: ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Algorithmic ideas: BUILD (Aho et al 81) bc|d ab|c R a  b   c  d d {a,b,c} a  b   c c {a,b} a  b  a b c b a d c b d c b a

Algorithmic ideas: limits of BUILD ,[object Object],d c b a c d b a R 2 bc|d bd|c ac|d ad|c ab|c ab|d a  b   c  d d c b a d b c a R 1 ab|c ac|b bc|d ab|d ac|d a  b   c  d d {a,b,c} a  b   c d c b a

Algorithmic ideas: PhySIC PC R bc|d bd|c ac|d ad|c ab|c ab|d R’ bc|d bd|c ac|d ad|c ab|c ab|d ,[object Object],[object Object],[object Object],[object Object],[object Object],Idea: temporarily forget the direct contradictions d c b a c d b a a  b   c  d  d a  b   c c d b a

Algorithmic ideas: limits of BUILD (2) ,[object Object],[object Object],ef|a ?? R ab|c ef|c c b a a  b   c  e  f {a,b} c {e,f} c f e a b c e f

Algorithmic ideas - a summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Primate case study: source trees ,[object Object],[object Object],[object Object],Anthropo ids

Primate case study: PC & PI in action ADRA2B IRBP Platyrrhines are unresolved due to a conflict (PC) PhySIC PC PhySIC Arbitrary resolution among Anthropo i ds is removed (PI) Source trees

Labels indicating source of problems ,[object Object],[object Object],[object Object],[object Object]

Pointing out “problems” in other supertrees ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Primate case study: MRP tree analyzed ADRA2B IRBP Source trees MRP supertree filtered MRP supertree 1 1 2 PC

Online server: http://atgc.lirmm.fr/SuperTree/PhySIC Contact: [email_address]

Conclusion & prospects ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Thanks ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Equipe Méth. et Algor. pour la bioinf. LIRMM Equipe Phylogénie Moléculaire ISEM

Phylogenetic Signal with Induction and non-Contradiction - V Berry

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Phylogenetic Signal with Induction and non-Contradiction - V Berry