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

2. Overview: Investigating the Tree of Life
Legless lizards have evolved independently in several different groups
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3. Figure 26.1
Figure 26.1 What is this organism?

4. Taxonomy- classification
Phylogeny is the evolutionary history of species
Systematics classifies organisms and determines their evolutionary relationships (evidence??)
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5. Linnaeus’ System Binomial Nomenclature Taxons Genus species
Ex: Homo sapiens
Taxons
DomainKingdomPhylumClassOrder
FamilyGenusSpecies
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6. Species: Panthera pardus Genus: Panthera Family: Felidae Order:
Figure 26.3
Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora
Class:
Mammalia
Figure 26.3 Linnaean classification.
Phylum:
Chordata
Kingdom:
Animalia
Domain:
Bacteria
Domain:
Archaea
Domain:
Eukarya

7. Each branch point represents the divergence of two species
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
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8. Order Family Genus Species Panthera pardus (leopard) Felidae Panthera
Figure 26.4
Order
Family
Genus
Species
Panthera
pardus
(leopard)
Felidae
Panthera
Taxidea
taxus
(American
badger)
Taxidea
Carnivora
Mustelidae
Lutra lutra
(European
otter)
Lutra
Figure 26.4 The connection between classification and phylogeny.
Canis
latrans
(coyote)
Canidae
Canis
Canis
lupus
(gray wolf)

9. where lineages diverge Taxon A
Figure 26.5
Branch point:
where lineages diverge
Taxon A
Taxon B
Sister
taxa
Taxon C
Taxon D
Taxon E
ANCESTRAL
LINEAGE
Taxon F
Figure 26.5 How to read a phylogenetic tree.
Basal
taxon
Taxon G
This branch point
represents the
common ancestor of
taxa A–G.
This branch point forms a
polytomy: an unresolved
pattern of divergence.

10. What We Can and Cannot Learn from Phylogenetic Trees
Phylogenetic trees show patterns of descent, not phenotypic similarity
Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage
It should not be assumed that a taxon evolved from the taxon next to it
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11. Minke (Southern Hemisphere)
Figure 26.6
RESULTS
Minke (Southern Hemisphere)
Unknowns #1a, 2, 3, 4, 5, 6, 7, 8
Minke (North Atlantic)
Unknown #9
Humpback (North Atlantic)
Humpback (North Pacific)
Unknown #1b
Gray
Figure 26.6 Inquiry: What is the species identity of food being sold as whale meat?
Blue
Unknowns #10, 11, 12
Unknown #13
Fin (Mediterranean)
Fin (Iceland)

12. Morphological and Molecular Homologies
Phenotypic and genetic similarities due to shared ancestry are called homologies
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13. 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
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14. Figure 26.7
Figure 26.7 Convergent evolution of analogous burrowing characteristics.

15. 1 1 2 Deletion 2 1 2 Insertion 3 1 2 4 1 2 Figure 26.8-4
Figure 26.8 Aligning segments of DNA. 2 4 1 2

16. Figure 26.9
Figure 26.9 A molecular homoplasy.

17. 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
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18. Monophyletic: the ancestor species and all its descendants
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19. A paraphyletic: ancestral species and some, but not all, of the descendants
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20. A polyphyletic: various species with different ancestors
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21. (a) Monophyletic group (clade) (b) Paraphyletic group
Figure 26.10
(a) Monophyletic group (clade)
(b) Paraphyletic group
(c) Polyphyletic group A A A B
Group  B B
Group  C C C D D D E E
Group  E
Figure Monophyletic, paraphyletic, and polyphyletic groups. F F F G G G

22. 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
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23. Figure 26.11
TAXA
Lancelet
(outgroup)
(outgroup)
Lancelet
Lamprey
Lamprey
Leopard
Bass
Frog
Turtle
Vertebral
column
(backbone) 1 1 1 1 1
Bass
Vertebral
column
Hinged jaws 1 1 1 1
Frog
Hinged jaws
Four walking
legs
CHARACTERS 1 1 1
Turtle
Four walking legs
Amnion 1 1
Figure Constructing a phylogenetic tree.
Amnion
Hair 1
Leopard
Hair
(a) Character table
(b) Phylogenetic tree

24. Length represents # differences
Figure 26.12
Length represents # differences
Drosophila
Lancelet
Zebrafish
Frog
Chicken
Figure Branch lengths can represent genetic change.
Human
Mouse

25. Length represents time
Figure 26.13
Length represents 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

26. Maximum parsimony assumes the tree with the fewest evolutionary events is the most likely
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27. (a) Percentage differences between sequences
Figure 26.14
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

28. Computer programs are used to search for trees that are parsimonious and likely
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29. Figure 26.15
TECHNIQUE
Species 
Species 
Species  1
Three phylogenetic hypotheses:  
 
 
   2
Site 1 2 3 4
Species  C T A T
Species  C T T C
Species  A G A C
Ancestral sequence A G T T 3
1/C
1/C  
 
 
1/C
  
Figure Research Method: Applying parsimony to a problem in molecular systematics
1/C
1/C 4
3/A
2/T
3/A
2/T 
3/A 
4/C
 
 
4/C
4/C
2/T
  
3/A
4/C
2/T
4/C
2/T
3/A
RESULTS  
 
 
  
6 events
7 events
7 events

30. Animation: The Geologic Record Right-click slide / select “Play”
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31. (b) Artist’s reconstruction of the dinosaur’s
Figure 26.17
Front limb
Hind limb
Figure Fossil support for a phylogenetic prediction: Dinosaurs built nests and brooded their eggs.
Eggs
(a) Fossil remains of
Oviraptor and eggs
(b) Artist’s reconstruction of the dinosaur’s
posture based on the fossil findings

32. 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 approach 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
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33. Speciation with divergence of gene
Figure 26.18
Formation of orthologous genes:
a product of speciation
Formation of paralogous genes:
within a species
Ancestral gene
Ancestral gene
Ancestral species
Species C
Speciation with
divergence of gene
Gene duplication and divergence
Figure Two types of homologous genes.
Orthologous genes
Paralogous genes
Species A
Species B
Species C after many generations

34. Gene number and the complexity of an organism are not strongly linked
For example, humans have only four times as many genes as yeast, a single-celled eukaryote
Genes in complex organisms appear to be very versatile, and each gene can perform many functions
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35. 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
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36. 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
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37. Individual genes vary in how clocklike they are
Molecular clocks are calibrated against branches whose dates are known from the fossil record
Individual genes vary in how clocklike they are
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38. Divergence time (millions of years)
Figure 26.19 90 60
Number of mutations 30
Figure A molecular clock for mammals. 30 60 90
120
Divergence time (millions of years)

39. Neutral Theory
Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and is not influenced by natural selection
It states that the rate of molecular change in these genes and proteins should be regular like a clock
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40. Problems 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
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41. Applying a Molecular Clock: The Origin of HIV
Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
HIV spread to humans more than once
Comparison of HIV samples 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
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42. Index of base changes between HIV gene sequences
Figure 26.20
0.20
0.15
HIV
Index of base changes between HIV gene sequences
0.10
Range
Adjusted best-fit line
(accounts for uncertain
dates of HIV sequences)
Figure Dating the origin of HIV-1 M with a molecular clock.
0.05
1900
1920
1940
1960
1980
2000
Year

43. 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
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44. 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 Classification Schemes genomes
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45. Animation: Classification Schemes Right-click slide / select “Play”
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46. Eukarya Bacteria Archaea Figure 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)

47. 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
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48. Horizontal gene transfer complicates efforts to build a tree of life
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 occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms
Horizontal gene transfer complicates efforts to build a tree of life
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49. Bacteria Eukarya Archaea 4 3 2 1 Billions of years ago Figure 26.22
Figure The role of horizontal gene transfer in the history of life. 4 3 2 1
Billions of years ago

50. Is the Tree of Life Really a Ring?
Some researchers suggest that eukaryotes arose as a fusion 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
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51. Figure 26.23
Archaea
Eukarya
Figure A ring of life.
Bacteria

52. A B D B D C C C B D A A (a) (b) (c) Figure 26.UN01
Figure 26.UN01 Concept Check 26.1, question 3
(a)
(b)
(c)

53. Branch point Taxon A Most recent common ancestor Taxon B Sister taxa
Figure 26.UN02
Branch point
Taxon A
Most recent
common
ancestor
Taxon B
Sister taxa
Taxon C
Taxon D
Taxon E
Figure 26.UN02 Summary figure, Concept 26.1
Polytomy
Taxon F
Taxon G
Basal taxon

54. Monophyletic group Polyphyletic group A A A B B B C C C D D D E E E F
Figure 26.UN03
Monophyletic group
Polyphyletic group A A A B B B C C C D D D E E E
Figure 26.UN03 Summary figure, Concept 26.3 F F F G G G
Paraphyletic group

55. Salamander Lizard Goat Human Figure 26.UN04
Figure 26.UN04 Test Your Understanding, question 5
Human

56. Figure 26.UN05
Figure 26.UN05 Test Your Understanding, question 9

57. Figure 26.UN06
Figure 26.UN06 Appendix A: answer to Figure 26.5 legend question

58. Figure 26.UN07
Figure 26.UN07 Appendix A: answer to Figure legend question

59. Figure 26.UN08
Figure 26.UN08 Appendix A: answer to Concept Check 26.1, question 4

60. Figure 26.UN09
Figure 26.UN09 Appendix A: answer to Concept Check 26.3, question 3

61. Figure 26.UN10
Figure 26.UN10 Appendix A: answer to Concept Check 26.6, question 3

62. Figure 26.UN11
Figure 26.UN11 Appendix A: answer to Test Your Understanding, question 9