Phylogeography
 Phylogenetics
o Understanding phylogenetic trees
o Major approaches to determining
phylogenies
 Phylogeography
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
F
G
H
I
J
K
L
M
N
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
Phylogenetic Tree Terms
Group, cluster, clade
Leaves, Operational
Taxonomic Units (OTUs)
terminal branches
A
B
C
D
E
F
node
interior
branches
ROOT
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
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
Monophyletic
group
G
Rooting with D as
outgroup
A
F
E
B
D
C
A
B
C
G
E
F
D
G
Now with C as
outgroup
A
F
E
B
D
C
A
B
G
E
C
G
F
E
D
F
A
B
D
C
Which of these four trees is
different?
Baum et al.
Phenetics (distance) vs Cladistics
(character state based)
Lowe, Harris, and Ashton 2004
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
9
9
10
9
7
8
5
11
11
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
Example: Brown Bears (Ursus arctos)
 Reduced to <1% of
original range in
North America
I
II
 Sequence mtDNA
control region of
bears from
worldwide
distribution
III
IV
 Notice unique
haplotype F in ABC
islands of Alaska
V
 Notice position of
polar bear
Avise 2004
Lowe, Harris, and Ashton 2004
Brown Bear Surprise
 Subsequent study of samples from ice cores
(36,000-43,000 years old) found all four
haplotypes
 How do you explain the modern distribution?
Current
Ancient
Brown Bears in North America (Ursus
arctos)
 Diversity assessed
based on 8
microsatellite loci
 Reduced diversity for
more isolated sites
(Kodiak, Yellowstone)
Brown Bear Nuclear Differentiation
 Assessed differentiation based on
17 nuclear microsatellite loci
 Strong differentiation between
Kodiak and Admiralty islands
Lowe, Harris, and Ashton 2004
Brown Bear Nuclear Differentiation
 Less differentiation for
nuclear than mitochondrial
markers
 Degree of differentiation
driven by distances
between islands: Admiralty
much more divergent than
Chicagof or Baranof
 Why?
GST
HS
 1
 1 HS
HT
Lowe, Harris, and Ashton 2004
 Also, maternal inheritance of mitochondrion
 Smaller effective population size of mitochondrion
 Mitochondrion is one locus: selective sweeps!
Ursus arctos in Europe
 Highly degraded populations, low
genetic diversity
 Haplotypes reveal 3 refugia
during glaciation
 Migration and admixture
following deglaciation (“suture
zones” in Scandinavia and central
Europe)
Taberlet et al. 1998;
Molecular Ecology 7:453
Human Phylogeography
 Most evidence points to origins in Africa and subsequent
migrations
Cavalli-Sforza 2003 Nature Genetics 33:266
Human
Phylogeography:
mtDNA
 Most ancient and diverse
haplotypes in Africa (dots)
 Migration and admixture is
evident from presence of
African haplotypes in other
clades
Human Phylogeography: X-chromosome
genes
 Pyruvate dehydrogenase E1
alpha subunit sequence
 25 polymorphic sites, 23 of
which were in African
sample
 African θ=6.9, non-African
θ=0.57
 Using chimp sequence as
outgroup, estimated that
divergence occurred 1.9
million years ago
Complexities to Human Phylogeography
 Some genes show evidence of Asian origin
 Sequence of X-linked ribonucleotide reductase M2 pseudogene 4
 Suggests single origin model is too simple: admixture and
selection?
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence of Admixture in Ancient
Eurasians
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence for Ancient Population Structure in
Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7:669
Evidence for Ancient Population Structure in
Nuclear but not Mitochondrial Trees
Garrigan 2007 Nature Reviews Genetics 7:669
Alternative Models to Single Origin
Garrigan 2007 Nature Reviews Genetics 7:669
Human Phylogeography with SNP
 Assayed 500,000 SNP genotypes for 3,192 Europeans
 Used Principal Components Analysis to ordinate samples in
space
 High correspondence betweeen sample ordination and
geographic origin of samples
 Individuals assigned
to populations of
origin with high
accuracy
Nested Clade Analysis

Combines spatial and temporal tests of
association

Can be used to distinguish ongoing
population processes from historical
events
Branco et al 2002 Evolution 56:792–803
Dc – Clade distance (measures geographic range of a
particular clade)
Dn – Nested clade distance (geographic relationship to
other same level categories)
I-T – average distance between interior and tip clades
within nested group
Use random permutation testing to test significance of associations
Templeton AR 1998 Molecular Ecology 7:381-397
Nested Clade Analysis - critique
and summary (reflections of a colleague)

Hardly anyone believes in it anyway (ie Wayne
Maddison is strongly against it, because it is too
conjectural - not statistically sound)

All you need to know is that people use it to make
conclusions about range expansions and historical
vicariant events, based on molecular data

The method replies on this inference key, which
ultimately tells you nothing in the end