Why do trees?

 

Phylogeny 101

• OTUs operational taxonomic units: species, populations, individuals

• Nodes internal (often ancestors)Nodes external (terminal, often living species,

individuals)• Branches length scaled

Branches length unscaled, nominal, arbitrary• Outgroup an OTU that is most distantly related

to all the other OTUs in the study.

Phylogeny 102• Trees rooted (N=(2n-3)! / 2n-2(n-2)!

Trees unrooted (N=(2n-5)! / 2n-3(n-3)!OTUs #rooted trees #unrooted trees2 1 13 3 14 15 35 105 156 954 1057 10395 9548 135135 103959 2027025 13513510 34349425 2027025

Trees NJ

• Distance matrix

• UPGMA assumes constant rate of evolution – molecular clock: don’t publish UPGMA trees

• Neighbor joining is very fast

• Often a “good enough” tree

• Embedded in ClustalW

• Use in publications only if too many taxa to compute with MP or ML

Distances from sequence

• Protdist/DNAdist

• Non-identical residues/total sequence length

• Correction for multiple hits necessary because 2 ID residues may be C -> T -> C

• Jukes-Cantor assumes all subs equally likely

• Kimura: transition rate NE transversion rate

• Ts usually > Tv

Trees MP

• Maximum parsimony

• Minimum # mutations to construct tree

• Better than NJ – information lost in distance matrix – but much slower

• Sensitive to long-branch attraction

• No explicit evolutionary model

• Protpars refuses to estimate branch lengths

• Informative sites

Trees ML

• Very CPU intensive• Requires explicit model of evolution – rate

and pattern of nucleotide substitution– JC Jukes/Cantor – K2P Kimura 2 parameter transition/transversion– F81 Felsenstein – base composition bias– HKY85 merges K2P and F81

• Explicit model -> preferred statistically• Assumes change more likely on long branch• No long-branch attraction• Wrong model -> wrong tree

Models of sequence evolution

HKY85

A C G T

A C G T

C A G T

G A C T

T A C G

 

Here we have a representative alignment. Want to determine the phylogenetic relationships among the

OTUs:

Site: 1 2 3 4 5 6 7 8 9OTU1 A A G A G T G C AOTU2 A G C C G T G C GOTU3 A G A T A T C C AOTU4 A G A G A T C C G * * *

It is a good alignment clearly aligning homologous sites without gaps.

There are 3 possible trees for 4 taxa (OTUs):

1 3 1 2 1 2 \_____/ \_____/ \_____/ / \ / \ / \ 2 4 3 4 4 3

Or (1,2)(3,4) (1,3)(2,4) and (1,4)(2,3)

Aim to identify (phylogenetically) informative sites and use these to determine which tree is most parsimonious.

The identical sites 1, 6, 8 are useless for phylogenetic purposes.

 

Site: 1 2 3 4 5 6 7 8 9

OTU1 A A G A G T G C A

OTU2 A G C C G T G C G

OTU3 A G A T A T C C A

OTU4 A G A G A T C C G

* * *

Site 2 also useless: OTU1’s A could be grouped with any of the Gs.

Site: 1 2 3 4 5 6 7 8 9OTU1 A A G A G T G C AOTU2 A G C C G T G C GOTU3 A G A T A T C C AOTU4 A G A G A T C C G * * *

Site 4 is uniformative as each site is different.UNLESS transitions weighted in which case (1,4)(2,3)

Site: 1 2 3 4 5 6 7 8 9

OTU1 A A G A G T G C A

OTU2 A G C C G T G C G

OTU3 A G A T A T C C A

OTU4 A G A G A T C C G

* * *

For site 3 each tree can be made with (minimum) 2 mutations:

Site: 1 2 3 4 5 6 7 8 9

OTU1 A A G A G T G C A

OTU2 A G C C G T G C G

OTU3 A G A T A T C C A

OTU4 A G A G A T C C G

* * *

(1,2)(3,4)

G A G A G A

\ / \ / \ /

G---A C---A A---A

/ \ / \ / \

C A C A C A

(1,3)(2,4)

G C can do worse:G C

\ / \ /

A---A G---A

/ \ / \

A A A A

(1,4)(2,3)

G C

\ /

A---A

/ \

A A

So site 3 is (Counterintuitively) NOT informative

Site 5, however is informative because one tree shortest.

Site: 1 2 3 4 5 6 7 8 9

OTU1 A A G A G T G C A

OTU2 A G C C G T G C G

OTU3 A G A T A T C C A

OTU4 A G A G A T C C G

* * *

(1,2)(3,4) (1,3)(2,4) (1,4)(2,3)

G A G G G G

\ / \ / \ /

G---A A---A G---G

/ \ / \ / \

G A A A A A

Likewise sites 7 and 9.By majority rule most parsimonious tree is

(1,2)(3,4) supported by 2/3 informative sites.

Site: 1 2 3 4 5 6 7 8 9

OTU1 A A G A G T G C A

OTU2 A G C C G T G C G

OTU3 A G A T A T C C A

OTU4 A G A G A T C C G

* * *

Protpars• infile:• 8 370• BRU MSQNSLRLVE DNSV-DKTKA LDAALSQIER • RLR ---------- ---V-DKSKA LEAALSQIER • NGR ---------- -MSD-DKSKA LAAALAQIEK • ECO ---------- AIDE-NKQKA LAAALGQIEK • YPR ---------M AIDE-NKQKA LAAALGQIEK • PSE ---------- -MDD-NKKRA LAAALGQIER • TTH ---------- -MEE-NKRKS LENALKTIEK • ACD ---------- -MDEPGGKIE FSPAFMQIEG

Protpars

• treefile:(((((ACD,TTH),(PSE,(YPR,ECO))),NGR),RLR),BRU);

• outfile:One most parsimonious tree found:

+-ACD +-------7 ! +-TTH +-6 ! ! +----PSE ! +----5 +-3 ! +-YPR ! ! +-4 ! ! +-ECO +-2 ! ! ! +-------------NGR--1 ! ! +----------------RLR ! +-------------------BRU

remember: this is an unrooted tree!

requires a total of 853.000

Clustalw

****** PHYLOGENETIC TREE MENU ******

1. Input an alignment 2. Exclude positions with gaps? = ON 3. Correct for multiple substitutions? = ON 4. Draw tree now 5. Bootstrap tree 6. Output format options

S. Execute a system command H. HELP or press [RETURN] to go back to main menu

ClustalW NJ• (((ACD:0.28958,

TTH:0.32705):0.03395,((BRU:0.07321,RLR:0.07032):0.11692,NGR:0.21168):0.02493):0.02092,(ECO:0.05022,YPR:0.05736):0.11997,PSE:0.15632);

• topologically the same as(((ACD,TTH),((BRU,RLR),NGR)),(ECO,YPR),PSE);

and cf: Protpars:(((((ACD,TTH),(PSE,(YPR,ECO))),NGR),RLR),BRU);

NJ vs ProtPars

Dealing with CDSs

• More info in DNA than proteins• Systematic 3rd posn changes can confuse• Use DNA directly only if evol dist short• For distant relationships: blank 3rd positions• Translate into protein to align

– then copygaps back to DNA

• Use dnadist with weights to investigate rates

Trees

General guidelines – NOT rules

• More data is better

• Excellent alignment = few informative sites

• Exclude unreliable data – toss all gaps?

• Use seqs/sites evolving at appropriate rate– Phylip DISTANCE– 3rd positions saturated– 2nd positions invariant– Fast evolving seqs for closely related taxa– Eliminate transition - homoplasy

Trees

• Beware base composition bias in unrealted taxa

• Are sites (hairpins?) independent?

• Are substitution rates equal across dataset?

• Long branches prone to error – remove them?