Building and visualizing phylogeny

Henrik LantzDept. of Medical Biochemistry and Microbiology, BMC, Uppsala University

MePhD in Plant Systematics, post

doc in Fungal SystematicsNow bioinformatician working

with genomic and transcriptomic data, mostly annotation of genomes

YouHow many of you have

experience with inferring phylogenies?

How many of you have experience with working with sequence data in the computer?

This lectureBasic facts about phylogenies

and nomenclature usedHow to infer a phylogeny from

sequence dataHow to visualize phylogenies

What is phylogeny?Evolutionary relationship of

organisms or genes – anything related by descent

Often visualized as a phylogenetic tree

From individual to phylogeny

Zoooooming out…

Overview

Organism based phylogeny

Gene families

A simple phylogeny

Branch

Node

Root

Time

A B C D

Root

C D A B

Root

Clades

A B C D

Root

C D A B

Root

Sister groups

A B C DE F G H

Sister-group relationships

Mouse Rabbit ChimpHumanBirds Kangaroo Horse Dog

A B C DE F G H

Monophyletic

Paraphyletic

Support values

Branch lengths

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!

Expasy

Phylogeny.fr

1. Fasta-format

>CO1_species1ACGTGTCCGA...>CO1_species2TCCGATGAAC...>CO1_species3GTGTCCGATC...Etc.

2. Alignment

From:>CO1_species1 ACGTGTCCGA>CO1_species2 TCCGATGAAC>CO1_species3 GTGTCCGATCTo:>CO1_species1 ACGTGTCCGA----->CO1_species2 -----TCCGATGAAC>CO1_species3 --GTGTCCGATC---

2. Alignment

>CO1_species1 ACGTGTCCGA----->CO1_species2 -----TCCGATGAAC>CO1_species3 --GTGTCCGATC--->CO1_species4 ACGTGACCGATC--->CO1_species5 -CGTGACCGATCAAC>CO1_species6 ACGTGTCCGATGAAC

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

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

3. Build the phylogeny - Phylogenetic methods

UPGMANeighbor joiningParsimonyLikelihood methods - Maximum Likelihood- Bayesian Methods

Do not use!Not recommendedOutdated

Use one of thesePhyml, Raxml

MrBayes

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

4. Visualization