Scribd
Upload
15 views48 pages

Phylogenetic Trees

The document provides an overview of phylogenetic trees, detailing the information they contain, such as relationships, traits, taxonomic labels, and time. It discusses how to use these trees in research, including creating them de novo and utilizing existing trees for various studies. Additionally, it offers insights into R coding for tree analysis and highlights important packages for evolutionary trait analysis.

Uploaded by

designers.hapi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
15 views48 pages

Phylogenetic Trees

The document provides an overview of phylogenetic trees, detailing the information they contain, such as relationships, traits, taxonomic labels, and time. It discusses how to use these trees in research, including creating them de novo and utilizing existing trees for various studies. Additionally, it offers insights into R coding for tree analysis and highlights important packages for evolutionary trait analysis.

Uploaded by

designers.hapi
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 48

UNDERSTANDING AND

USING PHYLOGENETIC
TREES IN YOUR RESEARCH

E Tuschhoff
Wiens lab
Tuesday Seminar 4/11
1. What information is
OUTLINE on trees?
2. Using trees in
research
3. R coding overview
WHAT INFORMATION
IS ON TREES?
border

wide gold

3 sides

blue

4 sides
C. ircle

T. riangleblue
65

100 T. rianglebrown

T. riangleplain

S. quarestripe
82

93 S. quareblue

S. quarered

10 mya 5 mya 0 mya


WHAT INFORMATION IS ON TREES?
C. ircle

Relationships T. riangleblue
65
Traits 100 T. rianglebrown

Taxonomic labels
T. riangleplain

Time
S. quarestripe

Ancestral 82

reconstructions 93 S. quareblue

Confidence S. quarered

10 mya 5 mya 0 mya


WAYS TO USE TREES
DISEASE
DYNAMICS
Ladner et al. 2020
MICRO
BIOMES
Moraitou et al.
2022
SPECIES
CO-OCCURRENCE
Barnagaud et al. 2014
COEVOLUTION

Wang et al. 2021


FUNCTIONAL
TRAITS
Floeter et al. 2017
FUNCTIONAL
TRAITS
Floeter et al. 2017
USING TREES IN
RESEARCH
CREATING TREES DE NOVO

• Relationships between organisms are


unknown
• Use a variety of traits
• Morphology
• Behavior
• Genetics
• Incorporate fossils and molecular clocks for
dating
USING EXISTING TREES

• Finding the right tree


• Broadness
• Detail
• Current hypotheses
FROG EXAMPLE: QUESTION

• Evolution of parental care in poison frogs


• Broadness: Include all dendrobatid frogs
• Detail: Tips represent species
FROG EXAMPLE: STEPS

1. Find a paper with a useful tree


2. Find the tree file
3. Download tree file and use
ALL FROGS

Feng et al. 2017


TOO BROAD

Feng et al. 2017


DENDROBATIDAE

Guillory et al. 2019


GOOD SCALE
TIPS ARE GENERA

Guillory et al. 2019


DENDROBATIDAE

Carvajal-Castro et al. 2021


GOOD SCALE
TIPS ARE SPECIES

Carvajal-Castro et al. 2021


FROG EXAMPLE: STEPS

1. Find a paper with a useful tree


a. Carvajal-Castro et al. 2021
2. Find the tree file
3. Download tree file and use
FROG EXAMPLE: FIND TREE

• Read methods of Carvajal-Castro et al. 2021


• Did they make their own tree?
• If yes, look in supplementary materials or data
accessibility statement
• If no, look at source paper
PHYLOGENETIC DATABASES

• Dryad: data repository with many trees


• Open Tree of Life: find supporting and
conflicting studies for nodes
• MorphoBank: matrices of morphological
characters and associated trees
• PhylomeDB: gene phylogenies
• DataOne: search across multiple databases
TREES IN R
TREE FORMATS

Newick:
• Tips
((A:1,B:2):3,C:4);
• Sister taxa
• Branch lengths
4

((A:1,B:2):3,C:4);

2
Tips
Sister taxa
3
Branch lengths

1
TREE FORMATS

• Phylip: includes multiple sequence


alignments
• NEXUS: includes comments and
additional information in blocks
PLOTTING A TREE IN R

Package: ape
Functions:
read.tree() for Newick trees
read.nexus() for NEXUS trees
plot.phylo() draw and adjust appearance
l i b ra r y(a p e )
m y t r < - r e a d. t ree ( t ex t = " ( (p a n:5 , h om o :5) : 2 ,g o ril l a :7 ) ;")
p l o t. p hyl o (my t r)
g e o < - fa c t or ( c(" A f ri c a", " Wo r ld" , "A f ric a " ))
m y c ol <- c ( "b l ue" , "r e d") [ g eo ]
p l o t. p hyl o (my t r, t i p. c olo r = m yco l)
a d d .s c ale . b ar ( )
a x i sP h ylo ( )
n o d el a bel s ( )
t i p la b els ( )
e d g el a bel s ( )
p l o t. p hyl o (my t r,x . l im = 12)
p h y da t apl o t (x , my t r , " m", o ff s et = 2, wid t h = 1)
• How fast are traits
ANSWERING evolving?
QUESTIONS • Are traits correlated
WITH with one another?
PHYLOGENIES • What were the
ancestral traits?
IMPORTANT PACKAGES

ape: Paradis et al. 2023


phangorn: Schliep et al. 2023
phytools: Revell 2023
RATES OF EVOLUTION

Package: geiger
Functions:
fitDiscrete() models vary by # of rates
fitContinuous() variety of models
fitContinuousMCMC() writes to BEAST-
friendly text file
TRAIT CORRELATIONS

Package: caper
Function:
pgls() linear model for continuous traits
TRAIT CORRELATIONS

Package: phytools
Function:
fitPagel() direction of effect for
binary traits
TRAIT RECONSTRUCTION

Package: ape
Function:
ace() continuous and discrete traits
TRAIT RECONSTRUCTION

Package: HiSSE
Function:
MarginReconHiSSE() probabilities of traits
at nodes and tips
TRAIT RECONSTRUCTION

Package: phangorn
Function:
ancestral.pml() no probabilities
• John Wiens
• Wiens lab
THANKS • Bronstein lab
UNDERSTANDING AND
USING PHYLOGENETIC
TREES IN YOUR RESEARCH

E Tuschhoff
Wiens lab
Tuesday Seminar 4/11

You might also like