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Transcript of Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC,...
![Page 1: Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.](https://reader034.fdocuments.us/reader034/viewer/2022042703/56649ee55503460f94bf453a/html5/thumbnails/1.jpg)
Building and visualizing phylogeny
Henrik LantzDept. of Medical Biochemistry and Microbiology, BMC, Uppsala University
![Page 2: Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.](https://reader034.fdocuments.us/reader034/viewer/2022042703/56649ee55503460f94bf453a/html5/thumbnails/2.jpg)
MePhD in Plant Systematics, post
doc in Fungal SystematicsNow bioinformatician working
with genomic and transcriptomic data, mostly annotation of genomes
![Page 3: Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.](https://reader034.fdocuments.us/reader034/viewer/2022042703/56649ee55503460f94bf453a/html5/thumbnails/3.jpg)
YouHow many of you have
experience with inferring phylogenies?
How many of you have experience with working with sequence data in the computer?
![Page 4: Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.](https://reader034.fdocuments.us/reader034/viewer/2022042703/56649ee55503460f94bf453a/html5/thumbnails/4.jpg)
This lectureBasic facts about phylogenies
and nomenclature usedHow to infer a phylogeny from
sequence dataHow to visualize phylogenies
![Page 5: Building and visualizing phylogeny Henrik Lantz Dept. of Medical Biochemistry and Microbiology, BMC, Uppsala University.](https://reader034.fdocuments.us/reader034/viewer/2022042703/56649ee55503460f94bf453a/html5/thumbnails/5.jpg)
What is phylogeny?Evolutionary relationship of
organisms or genes – anything related by descent
Often visualized as a phylogenetic tree
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From individual to phylogeny
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Zoooooming out…
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Overview
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Organism based phylogeny
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Gene families
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A simple phylogeny
Branch
Node
Root
Time
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A B C D
Root
C D A B
Root
Clades
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A B C D
Root
C D A B
Root
Sister groups
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A B C DE F G H
Sister-group relationships
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Mouse Rabbit ChimpHumanBirds Kangaroo Horse Dog
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A B C DE F G H
Monophyletic
Paraphyletic
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Support values
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Branch lengths
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Phylogeny 1-2-3
1. Sequence data, nucleotides or amino acids, in FASTA-format
2. Align the sequences3. Run the alignment in the
phylogeny program4. Visualize the results in a tree
viewer
Phylogeny.fr does all of this!
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Expasy
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Phylogeny.fr
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1. Fasta-format
>CO1_species1ACGTGTCCGA...>CO1_species2TCCGATGAAC...>CO1_species3GTGTCCGATC...Etc.
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2. Alignment
From:>CO1_species1 ACGTGTCCGA>CO1_species2 TCCGATGAAC>CO1_species3 GTGTCCGATCTo:>CO1_species1 ACGTGTCCGA----->CO1_species2 -----TCCGATGAAC>CO1_species3 --GTGTCCGATC---
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2. Alignment
>CO1_species1 ACGTGTCCGA----->CO1_species2 -----TCCGATGAAC>CO1_species3 --GTGTCCGATC--->CO1_species4 ACGTGACCGATC--->CO1_species5 -CGTGACCGATCAAC>CO1_species6 ACGTGTCCGATGAAC
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Homology and orthologyHomology - traits shared due to
common ancestry, e.g., fingered forelimbs in birds and mammals
Analogy - traits of similar function, but not due to shared ancestry, e.g., wings in birds and insects
Orthology - Sequences were split due to speciation events
Paralogy - Sequences were split due to duplication events
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OutgroupShould be something outside of
the study group. Used to orient the tree.
If you can, pick several taxa as outgroup
Most phylogenetic programs pick the upper-most sequence in your input-file as the outgroup unless you tell the program otherwise
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3. Build the phylogeny - Phylogenetic methods
UPGMANeighbor joiningParsimonyLikelihood methods - Maximum Likelihood- Bayesian Methods
Do not use!Not recommendedOutdated
Use one of thesePhyml, Raxml
MrBayes
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Substitution modelsJukes-Cantor - Transitions between all
nucleotides are the sameKimura - Different rates for transitions
and transversions (Purine AG, Pyrimidine CT)
GTR - Different rates for all transitions.Used by Phylogeny-frAmino acid models become much more complex as there are 20 states rather than 4
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4. Visualization