1. Chapter 4 The tree of life: how biologists use phylogeny to reconstruct the deep past

2. Readings
Read Chapter 4 of Zimmer and Emlen text

3. Phylogeny All living organisms are descended from a common ancestor.
If we can construct the evolutionary relationships between groups we can gain insight into history of evolutionary change.

4. Figure 4.2 Phylogenies at different scales
(A) The tree of life represents the historical relationships among all living things. Dashed lines represent hypothetical relationships. The entire animal kingdom is contained in the tiny yellow branch at far right (in the metazoans). Adapted from Delsuc et al. (2005). (B) A phylogeny of vertebrates. Adapted from the Center for North American Herpetology (2010). (C) A phylogeny of Micobacterium tuberculosis isolates from human patients around the globe. Adapted from Comas et al. (2010).
Figure 4.2 Phylogenies at different scales
Evolution, 1st Edition
Copyright © W.W. Norton & Company

5. A phylogeny is similar to a family tree

6. Phylogeny
Phylogeny is the study of the branching relationships between populations over evolutionary time.
A phylogenetic tree is built up by analyzing the distribution of traits across populations.

7. Traits (characters)
A trait (or character) is any observable characteristic of an organism (e.g. anatomical features, behaviors, gene sequences)

8. Traits
Traits are used to infer patterns of ancestry and descent among populations.
These patterns are then depicted in phylogenetic trees.

9. Mapping traits onto trees allows us to study the
We use traits both to reconstruct phylogenetic trees and to generate hypotheses about the timing of events in evolutionary history. (A) One set of traits—here genetic sequence data—is used to infer a phylogenetic tree for the species of interest. (B) A second set of traits, here flower color and morphology, are mapped onto the tree, helping us to reconstruct evolutionary events. The origin of the dark flower coloration is indicated by the filled horizontal bar. The origin of the novel flower shape is indicated by the open horizontal bar.
Mapping traits onto trees allows us to study the
sequence and timing (history) of evolutionary events.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.4 Traits and trees

10. Phylogenetic trees are hypotheses
Remember phylogenetic trees are hypotheses about the evolutionary relationships between groups.
New evidence can be used to test a tree.

11. How to read a phylogenetic tree
Each branch tip represents a taxon (a group of related organisms).
Interior nodes (where branches meet) represent common ancestors of the taxa at the ends of the branches.

12. Figure 4.6 Interior nodes represent common ancestors
Finding the common ancestor for a group involves tracing backward in time. Follow the dashed lines to see the common ancestors of different groups in this phylogeny.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.6 Interior nodes represent common ancestors

13. Ladder format Tree format
The two phylogenies of the vertebrates shown each illustrate exactly the same information. The phylogeny on the left (A) is sometimes referred to as a tree representation, whereas that on the right (B) is termed a ladder representation. In each, time flows from left to right, so that the branch tips at the right represent current groups, whereas the interior nodes (nodes on the inner section of the tree) represent ancestral populations. For example, the red dot indicates the common ancestor of birds and crocodilians, whereas the blue dot indicates the common ancestor to all tetrapods. The orange line segment is the root of the tree. Adapted from the Center for North American Herpetology (2010).
Tree format
Ladder format
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.5 Two equivalent ways of drawing a phylogeny

14. How to read a phylogenetic tree
Remember there are multiple different ways to depict relationship s in a phylogenetic tree.
Any node in a phylogenetic tree can be rotated without altering the relationships between taxa.

15. Figure 4.7 Rotating around any node leaves a phylogeny unchanged
Imagine that a phylogenetic tree was constructed of balls for nodes and sticks for branches. One could rotate any node 180° in space without changing the structure of the tree itself. The tree may look different, but notice that the relationships between nodes remain unaltered by the rotation.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.7 Rotating around any node leaves a phylogeny unchanged

16. Figure 4.8 Rotating phylogenetic trees
Whether a phylogeny is represented as a tree (A) or ladder (B), one can rotate at any node—or any combination of nodes—without changing the structure of the tree. Thus the leftmost tree shown in each row is identical from a phylogenetic perspective to the trees shown to the right. The colors indicate the nodes that were rotated in each case.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.8 Rotating phylogenetic trees

17. How to read a phylogenetic tree
We build phylogenetic trees to use to figure out evolutionary relationships between taxa and to identify “natural” groupings among taxa, those that reflect their true evolutionary relationships.
A key idea is that natural groupings called clades are monophyletic groups.

18. How to read a phylogenetic tree
Clade: a group of taxa that share a common ancestor.
Monophyletic group: consists of an ancestor and all of the taxa that are descendants of that ancestor.

19. Taxonomic units legitimate only if they represent a clade
Clades are monophyletic groups

21. How to read a phylogenetic tree
In the next slides elephants, manatees and hyraxes plus their common ancestor form a monophyletic group.
Similarly tapirs, rhinoceroses and horses plus their common ancestor form another monophyletic group.

22. Figure 4.11 Monophyletic clades of mammals
A partial phylogenetic tree of the mammals shows examples of monophyletic groups. Elephants, manatees, and hyraxes form one monophyletic group, tapirs and rhinoceroses form another, and the group of tapirs, rhinoceroses, and horses form a third. However, pachyderms– elephants, rhinoceroses, and hippopotamuses—are not a monophyletic group. Adapted from Murphy et al. (2001).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.11 Monophyletic clades of mammals

23. Polyphyletic group
A taxon is polyphyletic if it does not contain the most recent common ancestor of all members of the group.

25. Polyphyletic group
A polyphyletic group requires the group members to have each had an independent evolutionary origin of some diagnostic feature.
“poly” means many. Hence many origins in this case.

26. E.g. Referring to Elephants, rhinos, and hippos as“pachyderms.”
Pachyderms are a polyphyletic
group because each group
evolved thick skin separately.
A partial phylogenetic tree of the mammals shows examples of monophyletic groups. Elephants, manatees, and hyraxes form one monophyletic group, tapirs and rhinoceroses form another, and the group of tapirs, rhinoceroses, and horses form a third. However, pachyderms– elephants, rhinoceroses, and hippopotamuses—are not a monophyletic group. Adapted from Murphy et al. (2001).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Elephants, rhinos and hippos would form
polyphyletic group

27. Paraphyletic group
A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all of its descendents.

29. Paraphyletic group
An example of a paraphyletic group among vertebrates is“fish.”
All tetrapods (four-legged animals) are descended from lobe-finned fish ancestors, but are not considered “fish” hence “fish” is a paraphyletic group because the tetrapods are excluded.

30. Some Linnean classifications are not monophyletic

31. Figure 4.12 Phylogenetic tree of the vertebrates
The tetrapod vertebrates (bracketed in green) form one monophyletic group including birds, crocodilians, turtles, reptiles, mammals, and amphibians. Their unique common ancestor is circled in green. “Fish”—lampreys, cartilaginous fishes, ray-finned fishes, and lobe-finned fishes  are not a monophyletic group. Adapted from the Center for North American Herpetology (2010).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.12 Phylogenetic tree of the vertebrates

32. Rooted vs. unrooted trees
Trees we’ve seen so far have been rooted and these trees give a clear indication of the direction of time.
However, computer programs that produce phylogenetic trees often produce unrooted trees.

33. Rooted vs. unrooted trees
In an unrooted tree, branch tips are more recent than interior nodes, but you cannot tell which of multiple interior nodes is more recent than others.

34. Figure 4.13 Unrooted tree of proteobacteria
An unrooted tree illustrates the evolutionary relationships among the proteobacteria, a large group of bacteria including human- associated species such as E. coli and nitrogen- fixing species such as A. tumefaciens. Here we do not have enough information to say whether, for example, interior node A represents a more recent or less recent population than does interior node B. Adapted from Shin et al. (1993).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.13 Unrooted tree of proteobacteria

35. Rooted vs. unrooted trees
An unrooted tree can be rooted at any point and depending where it is rooted very different rooted trees will be produced.

36. Figure 4.14 Rooted trees from unrooted trees
An unrooted tree and three corresponding rooted trees. Each rooted tree is rooted around the labeled point on the unrooted tree.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.14 Rooted trees from unrooted trees

37. Rooted vs. unrooted trees
There is only one true tree of evolutionary relationships.
To identify that tree we must root the tree correctly.
Using an outgroup is the easiest way to root a tree.

38. Rooted vs. unrooted trees
An outgroup is a close relative of the members of the ingroup (the various species being studied) that provides a basis for comparison with the others.

39. Rooted vs. unrooted trees
The outgroup lets us know if a character state within the ingroup is ancestral or not.
If the outgroup and some of the ingroup possess a character state then that character state is considered ancestral.

40. Rooted vs. unrooted trees
Consider an unrooted tree of four magpie species.

41. Figure 5.15 Phylogeny of magpie populations.
(A) The black-billed magpie (Pica hudsonia). (B) An unrooted phylogenetic tree showing relationships among four magpie populations: the Korean magpie (Pica pica sericea), the Eurasian magpie (Pica pica pica), the black-billed magpie (Pica hudsonia), and the yellow-billed magpie (Pica nuttalli). This phylogeny is based on a maximum parsimony phylogeny derived using mitochondrial DNA sequences. Part B adapted from Lee et al. (2003).

42. Rooted vs. unrooted trees
To root the tree we need a group that split off earlier from the lineage that led to these four species of magpies.
Azure-winged magpie is a suitable outgroup. One this is added to the unrooted tree we can root the tree.

43. Figure 5.16a Rooting the magpie phylogeny using an outgroup.
The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).

44. Figure 5.16b Rooting the magpie phylogeny using an outgroup.
The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).

45. Branch lengths of trees
In some phylogenetic trees branches are drawn with different lengths.
In these trees branch lengths represent the amount of evolutionary change that has occurred in that lineage.

46. Figure 4.15 Cladograms and phylograms
Phylogenies can indicate evolutionary relationships only, or they can convey information regarding the amount of character change that has occurred along each branch. (A) A cladogram, such as this phylogeny of the primates, has the branch tips aligned and indicates only the evolutionary relationships among the species shown. (B) A phylogram indicates evolutionary relationships and also represents the amount of sequence change along each branch by means of differing branch lengths. Here we see a phylogram of primate lentiviruses, including human immunodeficiency viruses HIV-1 and HIV-2, and various forms of simian immunodeficiency virus (SIV). Adapted from Beer et al. (1999).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.15 Cladograms and phylograms

47. Building a phylogenetic tree--Homologous and analagous traits
Homologous traits are derived from a common ancestor.
E.g. all mammals possess hair. This is a homologous trait all mammals share because they inherited it from a common ancestor.
Analagous traits are shared by different species not because they were inherited from a common ancestor but because they evolved independently.

48. Figure 4.21 Homologous and analogous traits
(A) Long legs are a homologous trait as indicated in red; both long-legged species share a long-legged common ancestor. (B) Long tails are an analogous trait as indicated in blue; long tails evolved separately in the two long-tailed lineages, and their common ancestor presumably had a short tail.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.21 Homologous and analogous traits

49. Divergent evolution
Divergent evolution occurs when closely related populations diverge from each other because selection operates differently on them.
Such new species will possess many homologous traits in common.

50. Convegent Evolution
Analagous traits are the result of a process of convergent evolution whereby the same or similar solution to an evolutionary problem is converged upon by different organisms independently of each other.

51. Figure 4.22 Convergent evolution for coloration
Fence lizards and pocket mice have evolved similar patterns of cryptic coloration in each of three different habitats.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.22 Convergent evolution for coloration

52. Figure 4.23 Convergent evolution in body forms
The thunniform body design, which is well suited for open-ocean predators, represents an analogous trait when we compare tuna (left) and mako sharks (right). Adapted from Donley et al. (2004).
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.23 Convergent evolution in body forms

53. Synapomorphy
When building a phylogenetic tree we must use characters inherited from ancestors.
Such a character found in two or more taxa is referred to as a shared derived character or synapomorphy. Example B on the next slide is a synapomorphy.

54. (A) We say that the trait dark coloration is a derived trait when it has evolved from another trait, such as light coloration in this example. (B) When the derived trait is shared because of a pattern of common ancestry, we call it a shared derived trait or synapomorphy.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.24 Derived traits

55. Synapomorphy
If all shared traits were shared derived traits tree-building would be straightforward.
However, many traits are not e.g. analagous traits

56. Homoplasy
We want to avoid including analagous traits when constructing phylogenetic trees because they can mislead us.
An analagous trait in a tree is referred to as a homoplasy.

57. Not all traits are similar due to common descent
Homoplasy: character state similarity not due to common descent
Convergent evolution: independent evolution of similar trait
Evolutionary reversals: reversion back to an ancestral character state

58. Homoplasy
In the next slide (A) we do not know the ancestral color state so we have to represent it as unresolved (a polytomy).
If we know that our phylogenetic tree (B) correctly indicates the relationships between taxa then we know that dark coloration is a homoplasy having evolved independently twice.

59. Figure 4.25 An example of homoplasy
(A) If we know only the current character states and not the ancestral history, we represent this as a polytomy. (B) Dark coloration is an analogous trait in this phylogeny; we represent such a trait as a homoplasy.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.25 An example of homoplasy

60. Symplesiomorphy
Another way in which we could be mistaken is if a new trait arises in a lineage and is not shared with other taxa. This is called a symplesiomorphy.
In the next slide, light coloration has recently arisen in taxon 3. If we thought dark coloration was a shared derived character we would group species 1+2, (as in A) but it isn’t. Instead dark coloration is an ancestral trait and the correct phylogeny is shown in B.

61. Figure 4.26 Derived traits and symplesiomorphy
(A) If we mistakenly believe that dark coloration is a derived trait, this may not lead us to misinterpret the relationships among species 1, 2, and 3. (B) If a derived trait has arisen recently and appears in only one of the two most closely related species, the two more distantly related species share the same trait. In this case, we call the trait a symplesiomorphy.
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Figure 4.26 Derived traits and symplesiomorphy

62. Strategies to avoid homoplasies and symplesiomorphies
Several strategies exist to limit homoplasies and synapomorphies.
1. use traits that change relatively slowly in evolutionary time
2. use many traits to build the tree
3. use multiple outgroups to help identify ancestral values of traits.

63. Building a phylogeny of Carnivora (Box 4.1 in text)
The mammalian order Carnivora includes cats, dogs and other familiar predatory mammals.
Certain synapomorphies such as carnassial teeth (enlarged side teeth used to shear meat) unite the group, but there has been debate about relationships within the group.

64. Construction of phylogenies is based on analysis of characters
To analyze relationships among 10 species of carnivores we construct a data matrix of the distribution of a dozen traits across these taxa.

66. Clades are determined by synapomorphies
Using synapomorphies to identify clades we can construct a phylogentic tree. The numbers on the tree correspond to the character states in the matrix.
Some clades in tree are clearly defined but others not so well.

67. One point where relationships are unresolved.
Such uncertain branching is called a polytomy.

68. Adding data to the matrix
If we add a 13th trait to the data matrix we may be able to resolve the polytomy.
However, sometimes additional data doesn’t help or introduces more uncertainty.

70. Absence of a lower premolar is a character shared by cats, hyenas and otters, but that doesn’t fit with our previous tree.
Most likely this is a homoplasy (and the tooth was lost independently in different lineages).

72. In reality phylogentic analyses inevitably involved dealing with conflicting evidence.
The most commonly applied rule to resolve conflict is the principle of parsimony – choosing the simplest explanation i.e., the phylogeny that requires the fewest trait changes to construct it.

73. Consensus trees
Applying the principle of phylogeny to a larger (20 character) matrix of data reveals three equally parsimonious phylogenetic trees that differ somewhat from each other.
Notice, however, that certain portions of the tree are consistent across all three trees.
Using some mathematical analysis a consensus tree can be constructed that represents a “best estimate” of the true tree.

74. Three equally parsimonious trees (above)
Consensus tree (below).

75. Birds are dinosaurs: tracking the evolution of feathers and flight
Archaeopteryx, discovered in 1860, dates to 145 mya

76. Traits often change function over time
Traits often change function over time. Phylogenies allow us to track such changes over evolutionary time.
The oldest known fossil bird is Archaeopteryx (145mya), which possesses a suite of both avian and reptilian characteristics.

77. Birds today are defined by the possession of feathers and obviously they are used to fly, but phylogenetic analysis shows that this was not the original function of feathers as feathers are present in non-flying ancestral groups.
Phylogenetic analysis also reveals that birds evolved from dinosaurs.

79. Feather attachments on Velociraptor bones
Velociraptor ulna with
bumps resembling quill
nodes in living birds
(A+B)
Turkey Vulture ulna with
feathers attached to
quill nodes (C-F)

80. Feathers
Feathers must have played a different role in dinosaurs than flight.
Most likely they served as insulation and for display (functions they are still used for today in birds).

81. Feathers originally involved in other functions
Exaptation: natural selection co-opts a trait for a new function

82. Some practice problems working with phylogenetic trees

83. Find the most recent common ancestor of species 3,5 and 6
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Review Question 4.1

85. What would this tree look like if it were rotated around
(i) Node A (ii) Node B (iii) both nodes A + B?
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Review Question 4.3

86. Answers
(i) 1, 3, 2, 4, 5, 6
(ii) 1, 6, 5, 4, 3, 2
(iii) 1, 6, 5, 4, 2, 3

87. Which pairs of species are more closely related? 4&5 or 5&7?
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Review Question 4.5

88. Answers
(i) 5&7
(ii) 2&7
(iii) 3&5

89. According to the diagram which of these five traits do (i) sharks
(ii) turtles have?
Evolution, 1st Edition
Copyright © W.W. Norton & Company
Review Question 4.10

90. Answers
Shark : jaws
Turtle: jaws, dentary bone, lungs.

91. 2 3 1 A 4 5 6
Rooting the tree at A draw the rooted tree for the
above unrooted tree.

92. Answer 4 5 6 1 2 3 A

93. Do the other problems in your text!