1 / 29

Why do trees?

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

albany
Download Presentation

Why do trees?

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Why do trees?

  2. Phylogeny 101 • OTUs operational taxonomic units: species, populations, individuals • Nodes internal (often ancestors) Nodes external (terminal, often living species, individuals) • Branches length scaledBranches length unscaled, nominal, arbitrary • Outgroup an OTU that is most distantly related to all the other OTUs in the study.

  3. Phylogeny 102 • Trees rooted (N=(2n-3)! / 2n-2(n-2)!Trees unrooted (N=(2n-5)! / 2n-3(n-3)! OTUs #rooted trees #unrooted trees 2 1 1 3 3 1 4 15 3 5 105 15 6 954 105 7 10395 954 8 135135 10395 9 2027025 135135 10 34349425 2027025

  4. Trees NJ • Distancematrix • 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

  5. 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

  6. 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

  7. 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

  8. Models of sequence evolution HKY85 A C G T A pCbpGapTb C pAbpGbpTa G pAapCbpTb T pAbpCapGb

  9. Here we have a representative alignment. Want to determine the phylogenetic relationships among the OTUs: 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 * * * It is a good alignment clearly aligning homologous sites without gaps.

  10. 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.

  11. 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 * **

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

  13. 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 * * *

  14. 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 * * *

  15. (1,2)(3,4) G A G A G A \ / \ / \ / G---A C---A A---A / \ / \ / \ C A C A C A

  16. (1,3)(2,4) G C can do worse:G C \/ \ / A---A G---A / \ / \ A A A A

  17. (1,4)(2,3) G C \/ A---A / \ A A So site 3 is (Counterintuitively) NOT informative

  18. 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 * * *

  19. (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

  20. 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 * * *

  21. 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

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

  23. 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

  24. 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

  25. 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);

  26. NJ vs ProtPars

  27. 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

  28. 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

  29. 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?

More Related