Lecture 22 : Introduction to Phylogenetics
April 4, 2014
Last Time
Infinite alleles and stepwise
mutation models
Introduction to neutral theory
Molecular clock
Today
Introduction to phylogenetics
Phylogeography
Limitations of phylogenetic analysis
Coalescence introduction
Influence of demography on
coalescence time
Phylogenetics
 Study of the evolutionary relationships among individuals,
groups, or species
 Relationships often represented as dichotomous
branching tree
 Extremely common approach for detecting and displaying
relationships among genotypes
 Important in evolution, systematics, and ecology
(phylogeography)
Evolution
C
A
D
E
B
G
H
I
J
K
L
M
F
N
Slide adapted from Marta Riutart
O
P
Q
R
S
T
U
V
W
X
Y
Z
Ç
What is a phylogeny?
O
P
Q
R
S
T
U
V
W
X
Y
Z
Ç

Homology: similarity that is the result of inheritance from a common ancestor
Slide adapted from Marta Riutart
Phylogenetic Tree Terms
Group, cluster, clade
Leaves, Operational Taxonomic
Units (OTUs)
terminal branches
A
B
C
D
E
F
node
interior
branches
ROOT
Slide adapted from Marta Riutart
G
H
I
J
Tree Topology
Bacteria 1
Bacteria 2
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
(Bacteria1,(Bacteria2,Bacteria3),(Eukaryote1,((Eukaryote2,Eukaryote3),Eukaryote4)))
Bacteria 1
Bacteria 2
Bacteria 3
Eukaryote 1
Slide adapted from Marta Riutart
Eukaryote 2
Eukaryote 3
Eukaryote 4
Are these trees different?
How about these?
http://helix.biology.mcmaster.ca
Rooted versus Unrooted Trees
archaea
eukaryote
archaea
Unrooted tree
archaea
eukaryote
eukaryote
eukaryote
Rooted
by outgroup
bacteria outgroup
archaea
Monophyletic group
archaea
archaea
eukaryote
eukaryote
root
eukaryote
eukaryote
Slide adapted from Marta Riutart
Monophyletic
group
Rooting with D as
outgroup
G
A
F
E
B
D
C
A
B
C
G
E
F
Slide adapted from Marta Riutart
D
G
A
Now with C as outgroup
F
E
B
D
C
A
G
B
E
C
G
F
E
D
F
A
B
D
C
Which of these four trees is different?
Baum et al.
UPGMA Method
Use all pairwise
comparisons to make
dendrogram
UPGMA:Unweighted
Pairwise Groups
Method using
Arithmetic Means
Hierarchically link most
closely related
individuals
Read the Lab 11 Introduction!
Phenetics (distance) vs Cladistics
(character state based)
Lowe, Harris, and Ashton 2004
Parsimony Methods
 Based on underlying genealogical relationships among alleles
 Occam’s Razor: simplest scenario is the most likely
 Useful for depicting evolutionary relationships among taxa or
populations
 Choose tree that requires
smallest number of steps
(mutations) to produce
observed relationships
Choosing Phylogenetic Trees
MANY possible trees can be
built for a given set of taxa
Very computationally
intensive to choose among
these
Lowe, Harris, and Ashton 2004
UN 
(2n  5)!
2 n 3 (n  3)!
RN 
(2n  3)!
 (2n  3)U n
n2
2 (n  2)!
Choosing Phylogenetic Trees
Many algorithms exist for
searching tree space
Local optima are problem:
need to traverse valleys to
get to other peaks
Heuristic search: cut trees up
systematically and
reassemble
Branch and bound: search for
optimal path through tree
space
Felsenstein 2004
9
8
9
10
9
9
9
7
8
11
11
5
Choosing Phylogenetic Trees

If multiple trees equally likely, select majority rule or consensus

Strict consensus is most conservative approach

Bootstrap data matrix (sample with replacement) to determine
robustness of nodes
E
60
Lowe, Harris, and Ashton 2004
A
D F
CB
60
60
Felsenstein 2004
Phylogeography
 The study of evolutionary relationships among individuals based
on phylogenetic analysis of DNA sequences in geographic context
 Can be used to infer evolutionary history of populations
 Migrations
 Population subdivisions
 Bottlenecks/Founder Effects
 Can provide insights on current relationships among populations
 Connectedness of populations
 Effects of landscape features on gene flow
Phylogeography
Topology of tree provides
clues about evolutionary
and ecological history of a
set of populations
Dispersal creates poor
correspondence between
geography and tree
topology
Vicariance (division of
populations preventing
gene flow among
subpopulations) results in
neat mapping of geography
onto haplotypes
Example: Pocket gophers (Geomys pinetis)
 Fossorial rodent that inhabits
3-state area in the U.S.
 RFLP for mtDNA of 87
individuals revealed 23
haplotypes
 Parsimony network reveals
geographic relationships
among haplotypes
 Haplotypes generally
confined to single populations
 Major east-west split in
distribution revealed
Avise 2004
Problems with using Phylogenetics for
Inferring Evolution
 It
is a black box: starting from end point,
reconstructing past based on assumed
evolutionary model
 Homologs versus paralogs
 Hybridization
 Differential evolutionary rates
 Assumes coalescence
Gene Orthology
 Phylogenetics
requires unambiguous identification of
orthologous genes
 Paralogous genes are duplicated copies that do not share
a common evolutionary history
 Difficult to determine orthology relationships
paralogs
paralogs
Lowe, Harris, Ashton 2004
paralogs
orthologs