Module 4: Introduc/on to concepts and methods in molecular ... · Module 4: Introduc/on to concepts and methods in molecular phylogenecs Céline Poux Laboratoire EEP – UMR8198 Université

Module4:Introduc/ontoconceptsandmethodsinmolecularphylogene/cs

CélinePouxLaboratoireEEP–UMR8198

UniversitédeLille

Introduc/ontobioinforma/cs

SamuelBlanquartInria

LaboratoireCRIStAL–UMR9189UniversitédeLille

Introduc/ontobioinforma/cs

Part1:Introduc/on–PreparingthedatasetPart2:Phylogene/creconstruc/on–MLphylogene/creconstruc/onPart3:Reconstruc/onbiasesPart4:Phylogene/creconstruc/on–Bayesianreconstruc/on

Part5:Molecularda/ng–Bayesianda/ng

Reconstruc/onbiases

SignalOrthologouscharacters

Data

NoiseWheredoesitcomefrom?

POORSIGNAL LOTOFNOISEWRONGTREE

Data Alignment&cleaning TreebuildingEvolu/onarymodels Biases

Reconstruc/onbiases

1.   Stochas7cerrors: Samplingerrors

2. Systema7cerrors:

Methodologicalerrors

3. Biologicalerrors: Genestreesandspeciestreesarediscordant

Treereliability


Reconstruc/onbiases:thestochas/cerrors

Rokasetal.2003

Treereliability

106orthologousgenesfrom8yeastgenomes

Stochas7cerrorsaresamplingerrors

Thesamplingsizeoftheanalyzedcharactersistosmall



Rokasetal.2003

106genesdataset

12

34

5Nod

e3

Nod

e5

Treereliability



Data Alignment&cleaning TreebuildingEvolu/onarymodels BiasesDelsucetal.2005

Methodsforphylogenomicinference

Treereliability



=>Addingmoresequences–phylogenomics–isnotalwaysenoughtoresolveinconsistences

Philippeetal2011

Treereliability



Reconstruc/onbiases:thesystema/cerrors

Systema7cerrors:themethodofinferenceisinconsistent

ü  Thehypothesesofthereconstruc/onmethodsareviolatedü  Themodelsofsequencesevolu/onarenotaccurate.⇒ Mul/plessubs/tu/ons(homoplasy)cangoundetectedorbewrongly

inferred.

• Ratevaria/onamonglineage =>Longbranchaarac/on

• Ratevaria/onamongsites =>Satura/onatsomesites

• Heterogeneityofnucleo/decomposi/onamongspecies =>Composi/onalbiases

Treereliability



LongBranchAarac/on(LBA)

Yang&Rannala2012

Treereliability



Philippeetal.2007

MP11959AAsites

Treereliability

Tunicates




Philippeetal.2007

MP11959AAsites

Platyhelminthes

Tunicates

Treereliability




CATmixturemodel

TreereliabilityPhilippeetal.2007




Composi/onalbiases&Satura/on

Jeffroyetal.2006

Treereliability

BInt3 BInt

BInt12BIAA



Treereliability

Composi/onalbiases&Satura/on

(A)  Correctphylogeny.

(B)  Classicalreconstruc/onar/factwheremesophilicbacteriawithsimilarGCcontentclusterinthetree.

ARN16S

BlanquartetLar/llot2006


Reconstruc/onbiases:biologicalerrors

Genesphylogeny=Speciesphylogeny

Isthishypothesiscorrect?

Treereliability

@EmmanuelDouzery


Reconstruc/onbiases:Genesduplica/on

Pholetal.2009

Treereliability



Pholetal.2009

Treereliability



Treereliability@GuyPerrière

3.6.Orthologieetparalogie

Duplica/onSpecia/on

CopyA CopyB



Treereliability

Truephylogeny

@GuyPerrière



Treereliability


Truephylogeny

@GuyPerrière



Treereliability


Truephylogeny

Reconstructedphylogenyphylogeny

@GuyPerrière


Reconstruc/onbiases:Horizontalgenetransfer

CoverofMMBR,December2009

Treereliability

Reconstruc/onbiases:Horizontalgenetransfer

•  Horizontalgenestransfer:genestransmissionbetweendifferenttaxa.

•  Phenomenonfrequentbetweenprokaryotes.

•  Itimpliesvariousmechanisms:–Transforma/on,–Conjuga/on,–Transduc/on.17.6%ofthegenesE.coliwouldhavebeenacquiredbytransfer.

Data Alignment&cleaning TreebuildingEvolu/onarymodels BiasesTreereliability


Reconstruc/onbiases:horizontalgenetransfer

Calteauetal.2004

Treereliability

BacteriaArchea


Reconstruc/onbiases:Incompletelineagesor/ng&Ancestralpolymorphism

AdaptedfromLeliaertetal.2014

Treereliability

Data Alignment&cleaning TreebuildingEvolu/onarymodels BiasesAdaptedfromLeliaertetal.2014


Treereliability


Spe.A SpeB SpeC

Genetree=Speciestree



Treereliability


Spe.A SpeB SpeC

Genetree≠Speciestree



Treereliability



Treereliability



Treereliability


BC

ABC



Treereliability


AB

ABC



Treereliability


AB

ABC



Treereliability


Reconstruc/onbiases:Hybridiza/on&Genomeduplica/on

Macet-Houben&Gabaldon2015

Treereliability

Data Alignment&cleaning TreebuildingEvolu/onarymodels Branchsupports BiasesMacet-Houben&Gabaldon2015

Reconstruc/onbiases:Hybridiza/on&Genomeduplica/on

Concludingremarks


•  Thephylogene7csignaliscarriedbyorthologsequencesdisplayingsynapomorphiescharacteris/cofasharedevolu/vehistory.Thissignalincreaseswiththenumberofanalyzedcharacter.

•  Thenon-phylogene7csignalcanbedueto:•  Misalignedsequences,•  Saturatedsequences,•  GCcontentbiases,•  Simplis/corinappropriatemodelsofsequenceevolu/on,•  Comparisonofparalog,xenologorohnologsequences•  Incompletelineagesor/ng&ancestralpolymorphism

Treereliability

Concludingremarks


Strongphylogene/csignalWeaknon-phylogene/csignal

Weakphylogene/csignalWeaknon-phylogene/csignal

Weakphylogene/csignalStrongnon-phylogene/csignal

Correcttopology Resultsarenonsignificant Arctefactualtopologyrobustlyinferred

Treereliability

Reconstruc/onbiases


Advises:Ingeneral:ü  Usesinglecopygenes,ü  Checkincongruencesofindividualgenetreeswithspeciestree.

Fordeep/mephylogenies:ü  Checkthecomposi/onalbiases(Phylobayes)=>recodethedata,ü  Checkforhomoplasy(Phylobayes)=>removefastevolvingsites,ü  Includemorespecies(slowlyevolvingsequences,closelyrelatedoutgroup),

Fordeepcoalescenceproblems:ü  Mul/speciescoalescentmodels(*Beast)Forgeneduplica/onandlateralgenetransfer:ü  Phylogene/creconcilia/on(Phyldog)

Treereliability

Documents

Module 4: Introduc/on to concepts and methods in molecular ... · Module 4: Introduc/on to concepts and methods in molecular phylogenecs Céline Poux Laboratoire EEP – UMR8198 Université