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 2014 Slides 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. 25.18


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


Past



10

ab

cd

ef

gh

Present

Past



11

a

b

c

d

e

f

g

h

PresentPast

Horizontal Tree


Horizontal tree

12

Horizontal Tree


Horizontal tree

12

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. 25.114


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

fg

hi

jk


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

fg

hi

jk


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

rootQuestions

?????????


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. 25.140


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



h ggha b c d e f

Branch rotation

43

Consider this node

The node can rotate around freely



After rotation tree has same meaning

a b c d e f h g

Branch rotation

44



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 #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

47

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

48

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

49

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

50

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

51

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

52

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

53

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

54

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

55

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

56

Practice Question




Tree #1U V W X Y Z

Tree #2W V U Y Z X

Tree #3 U V W X Y Z

57

Practice Question




Tree #1U V W X Y Z

Tree #2W 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

• Groupings in trees ! 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

• 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







What kind of grouping are “reptiles”?

83

Practice Question







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





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




gha b c d e f

Practice Question

86



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


h

Practice Question



h


ga b c d e f

88


h

Practice Question



h


ga b c d e f

88



h

Practice Question



h


ga b c d e f

88



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



Practice Question



Bacteria + Archaea: includes MRCA but excludes some descendants

Practice Question




97

This pattern is called?

Practice Question




Bacteria and archaea a non-monophyletic group

98

This pattern is called?

Paraphyly


• Groupings in trees !Monophyletic groups !Non monophyletic groups !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


• Groupings in trees !Monophyletic groups !Non monophyletic groups !Relatedness ! Ingroups and outgroups


a b c d e h g f

Ingroup: the group of taxa under study

Ingroup

108

Key Concept: Ingroup


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

• Groupings in trees !Monophyletic groups !Non monophyletic groups !Relatedness ! Ingroups and outgroups ! “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

• Groupings in trees !Monophyletic groups !Non monophyletic groups !Relatedness ! Ingroups and outgroups ! “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

BC

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

Date post:	19-Jan-2017
Category:	Science
Upload:	jonathan-eisen
View:	392 times
Download:	2 times

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

Science