Download What is a phylogenetic tree? Phylogenetic trees

Lecture1.1
PhylogeneticTrees
IntroductiontoMolecularPhylogenetics
NathanLo
Whatisaphylogenetictree?
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Phylogenetictrees
Phylogeny:thetrue
evolutionary relationships
amongasetoforganisms
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Topology (relationships)
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Branchlengths(amountofevolutionary change ortime)
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Phylogenetictrees
Phylogenetictrees
Tip,leaf,orterminalnode
Root
Stemlineage
Clade
TOTAL
GROUP
Internalnode
(divergenceevent)
Sister
clade
Crowngroup
Branchoredge
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Phylogenetictrees
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Cladisticterms
Paraphyletic
Polytomy
Polyphyletic
Polytomies canbe
hard or soft
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Monophyletic
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Phylogenetictrees:Cladogram
Phylogenetictrees:Phylogram
Branch lengths
havenomeaning
Branchlengths
measureamount
ofevolutionary
change
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Phylogenetictrees:Chronogram
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Phylogenetictrees
Branch lengths
measuretime
(yrorMyr)
Vertical scaledoes
notrepresent anything
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Phylogenetictrees
Phylogenetictrees:Circular
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Rootisplacedincentre
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Cladogram, phylogram, or
chronogram
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Oftenusedto
displaylargetrees
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Difficult tointerpret
Rotatingaround nodes
doesnotchangethe
meaningofatree
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Phylogenetictrees:Circular
Jetz et al. (2012) Nature
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Phylogenetictrees:Unrooted
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Whenposition of
rootisunknown
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Rootbyincluding
outgroup taxa
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Rooting
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Include outgrouptaxa
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Taxoncloselyrelatedtoingroup
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Taxonisnotpartofingroup
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Without branchlengths(cladogram):
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Rootatmidpoint
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Phylogenetictrees:Newickformat
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Highlyunreliableifinternalbranchesareshort
Withbranchlengths(phylogram/chronogram):
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Useamolecularclock
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(Monotremes,(Marsupials,((Elephant,Armadillo),(((Squirrel,Rabbit),(Mo
nkey,Treeshrew)),(Shrew,(Whale,(Bat,(Cat,Rhinoceros))))))));
Automaticallyestimatespositionofroot
(Monotremes:12.0,(Marsupials:11.0,((Elephant:1.0,Armadillo:1.0):9.0,((
(Squirrel:1.0,Rabbit:1.0):2.0,(Monkey:1.0,Treeshrew:1.0):2.0):5.0,(Shre
w:4.0,(Whale:3.0,(Bat:2.0,(Cat:1.0,Rhinoceros:1.0):1.0):1.0):1.0):4.0):2.
0):1.0):1.0);
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Phylogeneticanalysis
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Molecularphylogenetics
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Sometimes weknowthephylogeny
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Viraltransmissionhistories
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Pedigrees(humans,domesticated animals,laborganisms,etc.)
Usuallywedonotknowthephylogeny butwecanestimateit
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Morphologicaldata
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Moleculardata
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Molecularphylogenetics
1.
Moleculardata
Datapreparation
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Select datatooptimise signal:noise
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Taxonandgenesampling
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Slowlyevolvingmarkersfordeepevolutionary events
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Datafiltering
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Rapidlyevolvingmarkersforrecentevolutionary events
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Sequence alignment
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Homoplasy
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2.
Phylogeneticinference
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Modelselection
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Estimationoftree
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Furtheranalysisandinterpretation
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Taxasharesimilaritiesthatdonotreflectevolutionaryhistory
Takeadvantage ofexistingresources
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Moleculardata
Single-nucleotidepolymorphisms
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Binarydata(presence/absence ofgenomic features)
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Singlesitessampledfromthroughout thegenome
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Microsatellites (repeat numbers)
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Morecommoninintraspecific (population) studies
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Single-nucleotide polymorphisms (SNPs)
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Reduced-representation sequences
Issuestoconsider:
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Sequence data
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Nucleotides
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Aminoacids
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Recombination
SNPsareusuallyunlinkedsotheyarelikelytohavedifferent
(gene)trees
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Ascertainmentbias
SNPsareselectedforvariabilityandthiscanmisleadestimatesof
populationsizes,rates,andotherparameters
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Reduced-representationsequences
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Markers identified bycuttinggenomewithrestriction enzymes
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Processcreates binarydataandshortsequences
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Examplesinclude RADseqandDArTseq
Sequencedata
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Issuestoconsider:
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Recombination
Markersareusuallyunlinkedsotheyare
likelytohavedifferent(gene)trees
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Missingdata
Typicallyalargeproportionofmissingdata
Codingsequences
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RibosomalRNA
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Protein-codinggenes
Non-coding sequences
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Intergenicsites
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Introns
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Oftenhaveindels(insertions/deletions)
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Needtoalignsequences
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Example:Whales
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DNAsequencealignment
InsertionofT
AACATTAGT
AACATTAGT
AACATTAGT
AACATAGGT
AACATAGGT
AACATAGGT
ACCAAAGT
ACCAAAGT
ACCA-AAGT
CACAAAT
CACA--AAT
ATAAACAA
ATAA-ACAA
AACATAAGT
AACAAAGT
AACAAAAT
AAAAAAAA
DeletionofA
CACAAAT
ATAAACAA
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DNAsequencealignment
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Homologous site
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Inherited fromthecommon
ancestor ofallsequences in
thealignment
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Theaimofsequence alignment
istomaximisethenumberof
sitesforwhich youcaninfer
homology
DNAsequencealignment
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AACATTAGT
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AACATAGGT
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ACCA-AAGT
Groupstogether thefirst
3sequences
Groupstogether thelast
2sequences
Informative forallphylogenetic
methods
AACATTAGT
AACATAGGT
ACCA-AAGT
CACA--AAT
CACA--AAT
ATAA-ACAA
ATAA-ACAA
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DNAsequencealignment
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Doesnotgroupanysequences
Notusefulformaximum
parsimony
AACATTAGT
Butinformative forestimating
amountofevolutionary change
AACATAGGT
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DNAsequencealignment
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Usefulforothermethods
ACCA-AAGT
CACA--AAT
ATAA-ACAA
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Indel– insertion ordeletion
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Potentially informative
AACATTAGT
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Mostphylogenetic methods
donotreally useindeldata
AACATAGGT
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Maximum-likelihood and
Bayesianmethodstypically
treattheminthesameway
asmissingdata
ACCA-AAGT
CACA--AAT
ATAA-ACAA
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Apracticalapproach
Apracticalapproach
Alignsequencesusingautomatedmethods
Alignsequencesusingautomatedmethods
Adjustalignmentsbyeye
CTATGTGGCACCCAGCCCATGCA--AGC
ATATGTGGCA-----CCCAGGCA--AGATATGTGGCACCCAGCCCATGCATTT-33
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Apracticalapproach
Apracticalapproach
Alignsequencesusingautomatedmethods
Alignsequencesusingautomatedmethods
Adjustalignmentsbyeye
Adjustalignmentsbyeye
Deletesiteswithuncertainhomology
Deletesiteswithuncertainhomology
CTATGTGGCACCCAGCCCATGCA--AGC
Furtherdatafiltering
ATATGTGGCA-----CCCAGGCA--AG-
?
ATATGTGGCACCCAGCCCATGCATTT-35
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Gapsandmissingdata
Deletesiteswithanymissingdata
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Potentiallossofinformative data
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Problematicinanalysesofdatasupermatrices
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Impactofmissingdataremainspoorly understood
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Filter dataaccording tochosenthreshold ofmissingdata
Treatgapsasunresolveddata
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Gene1 Gene2 Gene3 Gene4 Gene5
Gapissimultaneously A,C,G,andT
Taxon1
Mostcommonapproach
Taxon2
Taxon4
Notappropriatewhentherearelonggaps
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Maximise
gene
sampling
Taxon3
Treatgapsasa5th(nucleotide) or21st(aminoacid)state
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Gapsandmissingdata
Taxon5
Codegapsasbinarycharacters
Taxon6
Maximisetaxonsampling
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Mutationalsaturation
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Usefulreferences
Somesitescanevolve veryrapidly
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3rdcodonpositions
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LoopregionsinRNA
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Multiple hitscanerodephylogenetic signal
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Various waysoftestingforsaturation
Saturatedsitescanberemovedtoimprovesignal:noise
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Testyourunderstanding
Testyourunderstanding
Thenow-defunctmammalorderInsectivoraincludedtheshrewand
treeshrew.IsInsectivoramonophyletic, polyphyletic,orparaphyletic?
Thistreehas11taxa.How
manyinternalbranches
doesitcontain?
Whatisthesistertaxon to
thearmadillo?
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