BIS2C. Biodiversity and the Tree of Life. 2014. L2. Trees, taxa and groups.

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 2
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
Lecture 2:
!
Phylogeny 2:
Trees, Taxa, and Groups
!
Prof. Jonathan Eisen
1

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Where we are going and where we have been
• Previous lecture:
! 1: Introduction & Overview
• Current Lecture:
! 2: Trees, taxa and groups
• Next Lecture:
! 3: Characters and traits
2

Reading
• Previous lecture:
! 1: Chapter 22
• Current Lecture:
! 2: Chapter 22
• Next Lecture:
! 3: Chapter 22
3

Lecture 2 Outline
• Rotating phylogenetic trees
!
• Components of a phylogenetic tree
!
• Rotating branches in trees
!
• Groupings in trees
5

Lecture 2 Outline
6
!
!
!

Figure 22.1 The Components of a Phylogenetic Tree
7

Key Concept
Entire phylogenetic trees can be rotated in any
direction without changing their meaning.
Ch. 25.1
8

a b c d e f g h
A model phylogenetic tree
9

a b c d e f g h
Present
Past
9

a b c d e f g h
Present
Past
Vertical Tree
9

a b c d e f g h
Present
Past
Vertical Tree
Draw This Tree
9

10
a b c d e f g hPresent
Past

10
abcdefghPresent
Past

11
a
b
c
d
e
f
g
h
PresentPast
Horizontal Tree

Horizontal tree
12
Horizontal Tree

Horizontal tree
12
Horizontal TreeVertical Tree

Lecture 2 Outline
!
!
!
13

Key Concept
A phylogenetic tree is made up by combining
together a few simple units.
Ch. 25.1
14

a b c d e f g h
15
Present
Past

a b c d e f g h
16
a b c d e f g h

a b c d e f g h
17
a b c d e f g h
????

a b c d e f g h
a b c d e f g h
taxa
taxon: any group of species
that we designate a name
(p543) (e.g., a)
taxa: multiple taxons (e.g., a
and b) 18

Taxa
19
four taxa
(species)
three taxa
(domains)

a b c d e f g h
20
????

a b c d e f g h
21
nodes
f
g
h
i
j
k

a b c d e f g h
22
nodes
node:
(1) common ancestor of taxa “above” the node (e.g., f is common ancestor of a & b)
(2) splits in branches from one lineage into more
f
g
h
i
j
k

a b c d e f g h
23
????

a b c d e f g h
24
internal
nodes

a b c d e f g h
25
????

a b c d e f g h
26
root node

a b c d e f g h
27
root node
root node:
(1) common ancestor of all taxa in the tree
(2) point of earliest split in the tree

a b c d e f g h
28
????

a b c d e f g h
29
branches: represent the evolution of taxa over time
branches

a b c d e f g h
30
????

a b c d e f g h
31
internal
branches

a b c d e f g h
32
????

a b c d e f g h
33
terminal
branches

a b c d e f g h
34
????

a b c d e f g h
35
root or
root branch

a b c d e f g h
36
root: branch leading up to the root node (i.e., the common ancestor of all taxa in tree)
root or
root branch

Past
37
taxa
internal
branches
internal
nodes
root
node
terminal
branches
root

Past
38
taxa
internal
branches
internal
nodes
root
node
terminal
branches
root
Questions
?????????

Lecture 2 Outline
!
!
!
39

Key Concept: Rotation of Branches
Each node in a tree can be rotated/spun around
without changing the meaning of the tree. This is
known as “branch rotation”.
Ch. 25.1
40

a b c d e f g h
Branch rotation
41

a b c d e f g h
Branch rotation
42
“Order” left-to-right
has no specific
meaning on a
vertical tree

h ggha b c d e f
Branch rotation
43
Consider this
node
g h
The node
can rotate
around freely
has no specific
meaning on a
vertical tree

h ggha b c d e f
Branch rotation
43
Consider this
node
The node
can rotate
around freely
has no specific
meaning on a
vertical tree

After rotation tree has same meaning
a b c d e f h g
Branch rotation
44
has no specific
meaning on a
vertical tree

Figure 22.2 How to Read a Phylogenetic Tree (Part 2)
45

Practice Question
Practice Question
46

Consider the following three trees:
Which of these statements is true?
!
A) Tree #1 = Tree #2
B) Tree #1 = Tree #3
C) All three trees are equivalent
D) All three trees are different
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
47
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
48
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
49
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
50
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
51
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
52
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
53
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
54
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
55
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
56
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
57
Practice Question

!
Tree #1
U V W X Y Z
Tree #2
W V U Y Z X
Tree #3
U V W X Y Z
58
Practice Question

Lecture 2 Outline
!
!
!
5959

For many purposes it is useful to identify and name
organisms that all share a common ancestry to the exclusion
of other organisms
Common ancestry and naming
60

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 61
Where did HIV Come From?

Birds ARE Dinosaurs
62

Groupings in Trees: Monophyletic Groups
! Monophyletic groups
63

Monophyletic group:
(1) a group of organisms consisting of a single node and ALL
the descendants of that node in a tree and nothing else
(2) a group of organisms consisting of their most recent
common ancestor (MRCA) and all its descendants and
nothing else
!
Clade = a monophyletic group
Key Concept: Monophyletic Group
64

a b c d e h g f
Monophyly
65

a b c d e h g f
Monophyly
65
Consider node k
k

The group enclosed in
the yellow triangle is a
monophyletic group for
node k
a b c d e h g f
Monophyly
65
Consider node k
k

Practice Question
Practice Questions
66

How many monophyletic groups in this tree?*
a b c d e h g f
67
*In some senses, each taxon can be considered
to be a clade, we ignore these here
A: 1
B: 3
C: 5
D: 7
67
Practice Question

a b c d e h g f
68
*In some senses, each taxon can be considered
to be a clade, we ignore these here
A: 1
B: 3
C: 5
D: 7
68
Practice Question

a b c d e h g f
69
1: GH
69
Practice Question

a b c d e h g f
70
1: GH
2: GHF
70
Practice Question

a b c d e h g f
71
1: GH
2: GHF
3: EFGH
71
Practice Question

a b c d e h g f
72
1: GH
2: GHF
3: EFGH
4: DEFGH
72
Practice Question

a b c d e h g f
73
1: GH
2: GHF
3: EFGH
4: DEFGH
5: AB
1: GH
2: GHF
3: EFGH
4: DEFGH
5: AB
73
Practice Question

a b c d e h g f
74
1: GH
2: GHF
3: EFGH
4: DEFGH
5: AB
6: ABC
74
Practice Question

a b c d e h g f
75
1: GH
2: GHF
3: EFGH
4: DEFGH
5: AB
6: ABC
7: ABCDEFGH
75
Practice Question

Figure 22.3. Clades Represent an Ancestor and All of Its Descendants
76

Groupings in Trees: Monophyletic Groups
! Non monophyletic groups
77

Non-monophyletic groups are groups that include some but
not all descendants of the most recent common ancestor
of that group
Non-Monophyletic groups
a b c d e h g f
Non monophyly
78

MRCA
e, h, g, f are
excluded
Paraphyletic group
a b c d e h g f
Key Concept: Paraphyletic Group
79
Paraphyletic group: a group of organisms consisting of
their MRCA but excluding some of its descendants

MRCA
Polyphyletic group
a b c d e h g f
Key Concept: Polyphyletic Group
Polyphyletic group: a group of organisms that excludes the
MRCA of the group
80

Practice Question
Practice Questions
81

Lizards (including
snakes)
TurtlesCrocodilians Birds
Why are Reptiles (in the traditional sense) paraphyletic?
Reptiles (in red, not
including birds)
Example of a paraphyletic group: Reptiles (traditional sense)
What kind of grouping are “reptiles”?
Practice Question

Lizards (including
snakes)
including birds)
What kind of grouping are “reptiles”?
83
Practice Question

Lizards (including
snakes)
including birds)
Paraphyletic Group
84
Practice Question

Practice Question
Practice Questions
85

gha b c d e f
Practice Question
86

Are h and g monophyletic?
gha b c d e f
Practice Question
86

gha b c d e f
Practice Question
86
1) Trace to most
recent common
ancestor (MRCA)

2) Create group
that includes
MRCA and all
descendants
gha b c d e f
Practice Question
86
1) Trace to most
recent common
ancestor (MRCA)

2) Create group
that includes
MRCA and all
descendants
gha b c d e f
Practice Question
86
1) Trace to most
recent common
ancestor (MRCA)3) Determine if any
other modern taxa
are in group

2) Create group
that includes
MRCA and all
descendants
gha b c d e f
Practice Question
86
1) Trace to most
recent common
other modern taxa
are in group
4) Answer?

Practice Question
Practice Question
87

ga b c d e f
88
h
Practice Question

Are h and f monophyletic?
h ga b c d e f
88
h
Practice Question

h ga b c d e f
88
1) Trace to most
recent common
ancestor (MRCA)
h
Practice Question

h
2) Create group
that includes
MRCA and all
descendants
ga b c d e f
88
1) Trace to most
recent common
ancestor (MRCA)
h
Practice Question

h
2) Create group
that includes
MRCA and all
descendants
ga b c d e f
88
1) Trace to most
recent common
other modern taxa
are in group
h
Practice Question

h
2) Create group
that includes
MRCA and all
descendants
ga b c d e f
88
1) Trace to most
recent common
other modern taxa
are in group
4) Answer?
h
Practice Question

Practice Question
Practice Questions
89

Which of the
following are NOT
monophyletic?
A) ehgf
B) dehgf
C) bc
D) abcdehgf
a b c d e h g f
90
Practice Question

a b c d e h g f
91
Which of the
following are NOT
monophyletic?
A) ehgf
B) dehgf
C) bc
D) abcdehgf
Practice Question

Practice Question
Practice Question
92

Unicellular
eukaryotes
93
Practice Question

In the previous slide and lecture, a summary of the tree
of life was presented
!
Based on that tree, which of the following groups is NOT
monophyletic?
!
A. bacteria + archaea
B. archaea + eukaryotes
C. fungi
D. animals
E. plants
94
Practice Question

Unicellular
eukaryotes
Practice Question

Unicellular
eukaryotes
Bacteria + Archaea:
includes MRCA but
excludes some
descendants
Practice Question

Unicellular
eukaryotes
Bacteria + Archaea:
includes MRCA but
excludes some
descendants
97
This pattern is
called?
Practice Question

Unicellular
eukaryotes
Bacteria + Archaea:
includes MRCA but
excludes some
descendants
Bacteria and archaea a non-monophyletic group
98
This pattern is
called?
Paraphyly

! Relatedness

Key Concept: Relatedness
• Relatedness (in phylogenetics) is assessed by
examining patterns of common ancestry on a tree
100

Practice Question
Practice Question
101

a b c d e f h g
Is taxon e more closely related to d or g?
102
Practice Question

a b c d e f h g
103
This is answered to determining with which it
shares a more recent common ancestor
Is taxon e more closely related to d or g?
Practice Question

a b c d e f h g
104
e-g common
ancestor
Practice Question

a b c d e f h g
105
e-g common
ancestor
e-d common ancestor
Practice Question

a b c d e f h g
106
e-g common
ancestor
e-d common ancestor
e is more closely related to g than it is to d
Practice Question

! Relatedness
! Ingroups and outgroups

108
a b c d e h g f
Ingroup: the group of taxa
under study
Ingroup
108
Key Concept: Ingroup

109
Outgroup: one or more
taxa that are not members
of the ingroup.
a b c d e h g f
Ingroup
m n
Outgroups
109
Key Concept: Outgroup

Lecture 2 Outline
110
! Relatedness
! “Sisters”

a b c d e h g f
Sister groups: two clades or species that are each other’s
closest relatives (the two descendants of a single node)
Key Concept: Sister groups
111111

a b c d e h g f
g and h are “sisters” or “sister taxa”
112112

a b c d e h g f
113
The group “g and h” is sister to f
f is sister to the group “g and h”
113

Practice Question
Practice Question
114114

a b c d e h g f
What is the sister group of defgh?
115115
Practice Question

a b c d e h g f
Answer: abc
116116
Practice Question

a b c d e h g f
Answer: abc
By definition sister groups originate as lineages at the same
time.
Time of origination
117117
Practice Question

Lecture 2 Outline
118
! Relatedness
! “Sisters”
! Polytomies

a b c d e f h g
Our default tree
119119

a b c d e f h g
Key Concept: Polytomy
120
* Polytomies are used to indicate ambiguity in the branching patterns.
* Here the branching order among d-e-f-h-g is unknown. 
* In a polytomy, more than three branches connect to a node.
polytomy
120

Polytomy
121
So far we have been discussing bifurcating trees
These are trees in which each internal node gives rise to two
descendant branches.

Bifurcating Tree
122
Bifurcating trees - each internal node gives rise to two
descendant branches.

Polytomy
123
polytomy
Polytomies - some nodes have three or more descendant branches -
usually reflect uncertainty about phylogenetic relationships.

Extreme Polytomy
124
polytomy

Polytomy
125
polytomy
Three possible resolutions

Resolution 1:The beetle is more closely related
to (fly + moth) than the wasp is
polytomy
*

*
Resolution 1:The beetle is more closely related
to (fly + moth) than the wasp is

polytomy
Resolution 2:The wasp is more closely related
to (fly + moth) than the beetle
*

Resolution 2:The wasp is more closely related
to (fly + moth) than the beetle
*

polytomy
What is the third possibility?

Resolution 3: Wasp and beetle are each others closest
relatives

A B C D
A
B
C
D
A B C D
Units of
character
divergence
Units of
time
Cladogram Phylogram Chronogram
Different kinds of trees
Only the relative
branching order
is depicted. No
meaning to
branch lengths.
Branch length is
proportional to
the amount of
character change
Branch length is
proportional to
time

BIS2C. Biodiversity and the Tree of Life. 2014. L2. Trees, taxa and groups.

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