1. Phylogeny and the Tree of Life
Chapter 26
Phylogeny and the Tree of Life

2. Fig. 26-1
Figure 26.1 What is this organism?

3. Overview: Investigating the Tree of Life
Phylogeny is the evolutionary history of a species or group of related species
The discipline of systematics classifies organisms and determines their evolutionary relationships
Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

4. Fig. 26-2
Figure 26.2 An unexpected family tree

5. Concept 26.1: Phylogenies show evolutionary relationships
Taxonomy is the ordered division and naming of organisms

6. Binomial Nomenclature
In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
Two key features of his system remain useful today: two-part names for species and hierarchical classification

7. The two-part scientific name of a species is called a binomial
The first part of the name is the genus
The second part, called the specific epithet, is unique for each species within the genus
The first letter of the genus is capitalized, and the entire species name is italicized
Both parts together name the species (not the specific epithet alone)

8. Hierarchical Classification
Linnaeus introduced a system for grouping species in increasingly broad categories
The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
A taxonomic unit at any level of hierarchy is called a taxon

9. Figure 26.3 Hierarchical classification
Species:
Panthera
pardus
Genus: Panthera
Family: Felidae
Order: Carnivora
Class: Mammalia
Phylum: Chordata
Kingdom: Animalia
Archaea
Domain: Eukarya
Bacteria
Figure 26.3 Hierarchical classification

10. Class: Mammalia Phylum: Chordata Kingdom: Animalia Bacteria
Fig. 26-3a
Class: Mammalia
Phylum: Chordata
Figure 26.3 Hierarchical classification
Kingdom: Animalia
Bacteria
Domain: Eukarya
Archaea

11. Species: Panthera pardus Genus: Panthera Family: Felidae
Fig. 26-3b
Species:
Panthera
pardus
Genus: Panthera
Figure 26.3 Hierarchical classification
Family: Felidae
Order: Carnivora

12. Linking Classification and Phylogeny
Systematists depict evolutionary relationships in branching phylogenetic trees

13. Canis lupus Order Family Genus Species Felidae Panthera Pantherapardus
Fig. 26-4
Order
Family
Genus
Species
Felidae
Panthera
Pantherapardus
Taxidea
Taxidea
taxus
Carnivora
Mustelidae
Lutra lutra
Lutra
Figure 26.4 The connection between classification and phylogeny
Canis
latrans
Canidae
Canis
Canis
lupus

14. Linnaean classification and phylogeny can differ from each other
Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents

15. A phylogenetic tree represents a hypothesis about evolutionary relationships
Each branch point represents the divergence of two species
Sister taxa are groups that share an immediate common ancestor

16. A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
A polytomy is a branch from which more than two groups emerge

17. Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL
Fig. 26-5
Branch point
(node)
Taxon A
Taxon B
Sister
taxa
Taxon C
ANCESTRAL
LINEAGE
Taxon D
Taxon E
Figure 26.5 How to read a phylogenetic tree
Taxon F
Common ancestor of
taxa A–F
Polytomy

18. What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees do show patterns of descent
Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage
It shouldn’t be assumed that a taxon evolved from the taxon next to it

19. Applying Phylogenies
Phylogeny provides important information about similar characteristics in closely related species
A phylogeny was used to identify the species of whale from which “whale meat” originated

20. Fig. 26-6
RESULTS
Minke
(Antarctica)
Minke
(Australia)
Unknown #1a,
2, 3, 4, 5, 6, 7, 8
Minke
(North Atlantic)
Unknown #9
Humpback
(North Atlantic)
Humpback
(North Pacific)
Unknown #1b
Gray
Blue
(North Atlantic)
Figure 26.6 What is the species identity of food being sold as whale meat?
Blue
(North Pacific)
Unknown #10,
11, 12
Unknown #13
Fin
(Mediterranean)
Fin (Iceland)

21. RESULTS Minke (Antarctica) Minke (Australia) Unknown #1a,
Fig. 26-6a
RESULTS
Minke
(Antarctica)
Minke
(Australia)
Unknown #1a,
2, 3, 4, 5, 6, 7, 8
Minke
(North Atlantic)
Figure 26.6 What is the species identity of food being sold as whale meat?
Unknown #9

22. Humpback (North Atlantic) Humpback (North Pacific) Unknown #1b Gray
Fig. 26-6b
Humpback
(North Atlantic)
Humpback
(North Pacific)
Unknown #1b
Gray
Figure 26.6 What is the species identity of food being sold as whale meat?
Blue
(North Atlantic)
Blue
(North Pacific)

23. Unknown #10, 11, 12 Unknown #13 Fin (Mediterranean) Fin (Iceland)
Fig. 26-6c
Unknown #10,
11, 12
Unknown #13
Fin
(Mediterranean)
Fin (Iceland)
Figure 26.6 What is the species identity of food being sold as whale meat?

24. Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax

25. Fig. 26-UN1 A B D B D C C C B D A A
(a)
(b)
(c)

26. Concept 26.2: Phylogenies are inferred from morphological and molecular data
To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms

27. Morphological and Molecular Homologies
Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

28. Sorting Homology from Analogy
When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
Homology is similarity due to shared ancestry
Analogy is similarity due to convergent evolution

29. Fig. 26-7
Figure 26.7 Convergent evolution of analogous burrowing characteristics

30. Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

31. Bat and bird wings are homologous as forelimbs, but analogous as functional wings
Analogous structures or molecular sequences that evolved independently are also called homoplasies
Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity
The more complex two similar structures are, the more likely it is that they are homologous

32. Evaluating Molecular Homologies
Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

33. Deletion Insertion 1 2 3 4 Fig. 26-8
Figure 26.8 Aligning segments of DNA 4

34. Fig. 26-8a 1
Deletion 2
Figure 26.8 Aligning segments of DNA
Insertion

35. Fig. 26-8b 3 4
Figure 26.8 Aligning segments of DNA

36. It is also important to distinguish homology from analogy in molecular similarities
Mathematical tools help to identify molecular homoplasies, or coincidences
Molecular systematics uses DNA and other molecular data to determine evolutionary relationships

37. Fig. 26-9
Figure 26.9 A molecular homoplasy

38. Concept 26.3: Shared characters are used to construct phylogenetic trees
Once homologous characters have been identified, they can be used to infer a phylogeny

39. Cladistics
Cladistics groups organisms by common descent
A clade is a group of species that includes an ancestral species and all its descendants
Clades can be nested in larger clades, but not all groupings of organisms qualify as clades

40. A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

41. (a) Monophyletic group (clade) (b) Paraphyletic group
Fig A A A B
Group I B B C C C D D D E E
Group II E
Group III F F F G G G
Figure Monophyletic, paraphyletic, and polyphyletic groups
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group

42. (a) Monophyletic group (clade)
Fig a A B
Group I C D E F
Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups G
(a) Monophyletic group (clade)

43. A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

44. (b) Paraphyletic group
Fig b A B C D
Group II E F
Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups G
(b) Paraphyletic group

45. A polyphyletic grouping consists of various species that lack a common ancestor

46. (c) Polyphyletic group
Fig c A B C D
Group III E F
Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups G
(c) Polyphyletic group

47. Shared Ancestral and Shared Derived Characters
In comparison with its ancestor, an organism has both shared and different characteristics

48. A shared ancestral character is a character that originated in an ancestor of the taxon
A shared derived character is an evolutionary novelty unique to a particular clade
A character can be both ancestral and derived, depending on the context

49. Inferring Phylogenies Using Derived Characters
When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

50. Figure 26.11 Constructing a phylogenetic tree
TAXA
Lancelet
(outgroup)
(outgroup)
Lancelet
Salamander
Lamprey
Leopard
Lamprey
Tuna
Turtle
Vertebral column
(backbone)
Tuna 1 1 1 1 1
Vertebral
column
Hinged jaws 1 1 1 1
Salamander
Hinged jaws
CHARACTERS
Four walking legs 1 1 1
Turtle
Four walking legs
Amniotic (shelled) egg 1 1
Figure Constructing a phylogenetic tree
Amniotic egg
Leopard
Hair 1
Hair
(a) Character table
(b) Phylogenetic tree

51. Amniotic (shelled) egg 1 1
Fig a
TAXA
(outgroup)
Lancelet
Salamander
Lamprey
Leopard
Tuna
Turtle
Vertebral column
(backbone) 1 1 1 1 1
Hinged jaws 1 1 1 1
CHARACTERS
Four walking legs 1 1 1
Figure Constructing a phylogenetic tree
Amniotic (shelled) egg 1 1
Hair 1
(a) Character table

52. Vertebral column Hinged jaws Four walking legs Amniotic egg Lancelet
Fig b
Lancelet
(outgroup)
Lamprey
Tuna
Vertebral
column
Salamander
Hinged jaws
Figure Constructing a phylogenetic tree
Turtle
Four walking legs
Amniotic egg
Leopard
Hair
(b) Phylogenetic tree

53. An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics

54. Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

55. Phylogenetic Trees with Proportional Branch Lengths
In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

56. Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Fig. 26-12
Figure Branch lengths can indicate relative amounts of genetic change
Mouse

57. In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

58. Figure 26.13 Branch lengths can indicate time
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Human
Figure Branch lengths can indicate time
Mouse
PALEOZOIC
MESOZOIC
CENOZOIC
542
251
65.5
Present
Millions of years ago

59. Maximum Parsimony and Maximum Likelihood
Systematists can never be sure of finding the best tree in a large data set
They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood

60. Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely
The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

61. (a) Percentage differences between sequences
Fig
Human
Mushroom
Tulip
Human
30%
40%
Mushroom
40%
Tulip
(a) Percentage differences between sequences
15% 5% 5%
Figure Trees with different likelihoods
15%
15%
10%
20%
25%
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees

62. (a) Percentage differences between sequences
Fig a
Human
Mushroom
Tulip
Human
30%
40%
Mushroom
40%
Tulip
Figure Trees with different likelihoods
(a) Percentage differences between sequences

63. (b) Comparison of possible trees
Fig b
15% 5% 5%
15%
15%
10%
20%
25%
Figure Trees with different likelihoods
Tree 1: More likely
Tree 2: Less likely
(b) Comparison of possible trees

64. Computer programs are used to search for trees that are parsimonious and likely

65. Three phylogenetic hypotheses: I I III
Fig
Species I
Species II
Species III
Three phylogenetic hypotheses:
Figure Applying parsimony to a problem in molecular systematics I I
III II
III II
III II I

66. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
Figure Applying parsimony to a problem in molecular systematics

67. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
3/A
2/T
3/A I I
III
2/T
3/A
4/C II
III II
4/C
4/C
2/T
III II I
3/A
4/C
2/T
4/C
2/T
3/A
Figure Applying parsimony to a problem in molecular systematics

68. Site 1 2 3 4 Species I C T A T I I III Species II C T T C II III II
Fig
Site 1 2 3 4
1/C
Species I C T A T I I
III
1/C
Species II C T T C II
III II
1/C
Species III A G A C
III II I
1/C
1/C
Ancestral
sequence A G T T
3/A
2/T
3/A I I
III
2/T
3/A
4/C II
III II
4/C
4/C
2/T
III II I
3/A
4/C
2/T
4/C
2/T
3/A
Figure Applying parsimony to a problem in molecular systematics I I
III II
III II
III II I
6 events
7 events
7 events

69. Phylogenetic Trees as Hypotheses
The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents

70. Lizards and snakes Crocodilians Ornithischian dinosaurs Common
Fig
Lizards
and snakes
Crocodilians
Ornithischian
dinosaurs
Common
ancestor of
crocodilians,
dinosaurs,
and birds
Saurischian
dinosaurs
lFigure A phylogenetic tree of birds and their close relatives
Birds

71. Animation: The Geologic Record
This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles
Animation: The Geologic Record

72. (a) Fossil remains of Oviraptor and eggs
Fig
Front limb
Hind limb
Eggs
(a) Fossil remains of Oviraptor
and eggs
Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
(b) Artist’s reconstruction of the dinosaur’s posture

73. (a) Fossil remains of Oviraptor and eggs
Fig a
Front limb
Hind limb
Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
Eggs
(a) Fossil remains of Oviraptor
and eggs

74. (b) Artist’s reconstruction of the dinosaur’s posture
Fig b
Figure Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
(b) Artist’s reconstruction of the dinosaur’s posture

75. Concept 26.4: An organism’s evolutionary history is documented in its genome
Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history
DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
mtDNA evolves rapidly and can be used to explore recent evolutionary events

76. Gene Duplications and Gene Families
Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
Like homologous genes, duplicated genes can be traced to a common ancestor

77. Orthologous genes are found in a single copy in the genome and are homologous between species
They can diverge only after speciation occurs

78. Paralogous genes result from gene duplication, so are found in more than one copy in the genome
They can diverge within the clade that carries them and often evolve new functions

79. Speciation with divergence of gene
Fig
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Orthologous genes
Species A
Species B
(a) Orthologous genes
Species A
Figure How two types of homologous genes originate
Gene duplication and divergence
Paralogous genes
Species A after many generations
(b) Paralogous genes

80. Speciation with divergence of gene
Fig a
Ancestral gene
Ancestral species
Speciation with
divergence of gene
Figure How two types of homologous genes originate
Orthologous genes
Species A
Species B
(a) Orthologous genes

81. Gene duplication and divergence
Fig b
Species A
Gene duplication and divergence
Figure How two types of homologous genes originate
Paralogous genes
Species A after many generations
(b) Paralogous genes

82. Genome Evolution
Orthologous genes are widespread and extend across many widely varied species
Gene number and the complexity of an organism are not strongly linked
Genes in complex organisms appear to be very versatile and each gene can perform many functions

83. Concept 26.5: Molecular clocks help track evolutionary time
To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

84. Molecular Clocks
A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor
In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated

85. Molecular clocks are calibrated against branches whose dates are known from the fossil record

86. Divergence time (millions of years)
Fig 90 60
Number of mutations 30
Figure A molecular clock for mammals 30 60 90
120
Divergence time (millions of years)

87. Neutral Theory
Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection
It states that the rate of molecular change in these genes and proteins should be regular like a clock

88. Difficulties with Molecular Clocks
The molecular clock does not run as smoothly as neutral theory predicts
Irregularities result from natural selection in which some DNA changes are favored over others
Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty
The use of multiple genes may improve estimates

89. Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way
Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

90. Index of base changes between HIV sequences
Fig
0.20
0.15
Computer model
of HIV
Index of base changes between HIV sequences
0.10
Range
Figure Dating the origin of HIV-1 M with a molecular clock
0.05
1900
1920
1940
1960
1980
2000
Year

91. Concept 26.6: New information continues to revise our understanding of the tree of life
Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

92. From Two Kingdoms to Three Domains
Early taxonomists classified all species as either plants or animals
Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
The three-domain system is supported by data from many sequenced genomes
Animation: Classification Schemes

93. EUKARYA BACTERIA ARCHAEA Fig. 26-21 Land plants Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi
Sulfolobus
Green nonsulfur bacteria
Thermophiles
(Mitochondrion)
Figure The three domains of life
Spirochetes
Halophiles
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
BACTERIA
Methanobacterium
Cyanobacteria
ARCHAEA
(Plastids, including
chloroplasts)

94. BACTERIA Green nonsulfur bacteria (Mitochondrion) Spirochetes
Fig a
Green nonsulfur bacteria
(Mitochondrion)
Spirochetes
Chlamydia
COMMON
ANCESTOR
OF ALL
LIFE
Green
sulfur bacteria
Figure The three domains of life
BACTERIA
Cyanobacteria
(Plastids, including
chloroplasts)

95. ARCHAEA Sulfolobus Thermophiles Halophiles Methanobacterium
Fig b
Sulfolobus
Thermophiles
Halophiles
Figure The three domains of life
Methanobacterium
ARCHAEA

96. EUKARYA Dinoflagellates Land plants Forams Ciliates Red algae Amoebas
Fig c
EUKARYA
Land plants
Dinoflagellates
Green algae
Forams
Ciliates
Diatoms
Red algae
Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Figure The three domains of life
Fungi

97. A Simple Tree of All Life
The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria
The tree of life is based largely on rRNA genes, as these have evolved slowly

98. There have been substantial interchanges of genes between organisms in different domains
Horizontal gene transfer is the movement of genes from one genome to another
Horizontal gene transfer complicates efforts to build a tree of life

99. Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Fig. 26-22
Figure The role of horizontal gene transfer in the history of life 4 3 2 1
Billions of years ago

100. Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean
If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

101. Fig
Eukarya
Bacteria
Archaea
Figure A ring of life

102. Node Taxon A Taxon B Sister taxa Taxon C Taxon D Taxon E Most recent
Fig. 26-UN2
Node
Taxon A
Taxon B
Sister taxa
Taxon C
Taxon D
Taxon E
Most recent
common
ancestor
Polytomy
Taxon F

103. Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Fig. 26-UN3
Monophyletic group A A A B B B C C C D D D E E E F F F G G G
Paraphyletic group
Polyphyletic group

104. Fig. 26-UN4
Salamander
Lizard
Goat
Human

105. Fig. 26-UN5

106. Fig. 26-UN6

107. Fig. 26-UN7

108. Fig. 26-UN8

109. Fig. 26-UN9

110. Fig. 26-UN10

111. Fig. 26-UN10a

112. Fig. 26-UN10b

113. You should now be able to:
Explain the justification for taxonomy based on a PhyloCode
Explain the importance of distinguishing between homology and analogy
Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes

114. Define horizontal gene transfer and explain how it complicates phylogenetic trees
Explain molecular clocks and discuss their limitations