1. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings PowerPoint ® Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp Chapter 26 Phylogeny and the Tree of Life

2. Fig. 26-1

3. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

5. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.1: Phylogenies show evolutionary relationships Taxonomy is the ordered division and naming of organisms

6. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia ArchaeaDomain: Eukarya Bacteria

10. Fig. 26-3a Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: EukaryaBacteria

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

12. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees

13. Fig. 26-4 Species Canis lupus Panthera pardus Taxidea taxus Lutra lutra Canis latrans OrderFamilyGenus Carnivora Felidae Mustelidae Canidae Canis Lutra Taxidea Panthera

14. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

16. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A phylogenetic tree represents a hypothesis about evolutionary relationships Each branch point, or node, represents the divergence of two or more species A node behind another node indicates a common ancestor that lived prior. Sister taxa are groups that share an immediate common ancestor

17. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings What We Can and Cannot Learn from Phylogenetic Trees * Phylogenetic trees may not indicate when a species evolved or how much genetic change occurred in a lineage. Old divisions were arbitrarily chosen by taxonomists using general homological evidence from studying morphology and fossils. * It shouldn’t be assumed that a taxon evolved from the taxon behind it, as we continually update by placing new species, finding extinct species, and in general examining current evidence.

18. Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C Taxon D Taxon E Taxon F

19. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Applying Phylogenies Ex: We know the closest living relatives of corn based on DNA data. They are two species of wild grasses we can use as “reserve” organisms of beneficial genes! Ex: A phylogeny was used to identify the species of whale from which “whale meat” originated. This proved illegal harvesting of endangered species was taking place. Ex: Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax

20. Fig. 26-6 Fin (Mediterranean) Fin (Iceland) RESULTS Unknown #10, 11, 12 Unknown #13 Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific) Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8

21. Fig. 26-6a Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 RESULTS

22. Fig. 26-6b Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific)

23. Fig. 26-6c Fin (Mediterranean) Fin (Iceland) Unknown #13 Unknown #10, 11, 12

24. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

26. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Sorting Homology from Analogy When constructing a phylogeny,we need to distinguish whether a similarity is the result of homology or analogy! Homology is similarity due to shared ancestry, from DIVERGENT evolution. Analogy is similarity due to CONVERGENT evolution.

29. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings CONVERGENT evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

30. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Which creatures/structures show convergency/analogy and which show divergency/homology? Last common ancestor-320 mya

31. Fig. 26-7 Australian marsupial (a mole-like mammal) North American MOLE (a eutherian) Last known common ancestor-140 mya

32. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

33. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Evaluating Molecular Homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

34. Fig. 26-8 Deletion Insertion 1 2 3 4

35. Fig. 26-8a Deletion Insertion 1 2

36. Fig. 26-8b 3 4

37. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

38. Fig. 26-9

39. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.3: Shared characters are used to construct phylogenetic trees Once homologous characteristics have been identified, they can be used to determine phylogeny (evolutionary history). Several species placed into a group that centers around a specific homologous characteristic is known as a CLADE. Clades include ancestral species and all of it’s descendants that share the ancestor’s specific characteristic identified. The study of clades is known as CLADISTICS.

40. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Cladistics Clades can be nested in larger clades, but not all groupings of organisms qualify as clades A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

41. Fig. 26-10a A B C D E F G Group I (a) Monophyletic group (clade)

42. Fig. 26-10 A A A BBB CCC D D D EEE FF F G GG Group III Group II Group I (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group Provide 1 example of a monophyletic clade using your previously drawn Carnivora tree.

43. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

44. Fig. 26-10b A B C D E F G Group II (b) Paraphyletic group

45. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A polyphyletic grouping consists of various species that lack a common ancestor

46. Fig. 26-10c A B C D E F G Group III (c) Polyphyletic group

47. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics

48. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Inferring Phylogenies Using Derived Characters When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

50. Fig. 26-11a TAXA Lancelet Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table

51. Fig. 26-11a TAXA Lancelet Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table 0 00 0 0 0 0 0 0 0 00 0 00 1 1 1 1 11 1 11 1 1 11 1 1

52. Fig. 26-11b Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup)

53. Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup) 0 00 0 0 0 00 0 0 00 000 1 11 1 1 1 1 11 1 1 11 11

54. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

55. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

56. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

57. Fig. 26-12 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse

58. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

59. Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present65.5 MESOZOIC 251 Millions of years ago PALEOZOIC 542

60. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

61. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

62. Fig. 26-14 Human 15% Tree 1: More likelyTree 2: Less likely (b) Comparison of possible trees 15% 5% 10% 25% 20% 40% 30%0 0 0 (a) Percentage differences between sequences Human Mushroom Tulip

63. Fig. 26-14a Human 40% 30% 0 0 0 (a) Percentage differences between sequences Human Mushroom Tulip

64. Fig. 26-14b 15% Tree 1: More likelyTree 2: Less likely (b) Comparison of possible trees 15% 5% 10% 25% 20%

65. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Computer programs are used to search for trees that are parsimonious and likely

66. Fig. 26-15-1 Species I Three phylogenetic hypotheses: Species II Species III I II III I I II III

67. Fig. 26-15-2 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G

68. Fig. 26-15-3 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G I I I II III 3/A 2/T 4/C

69. Fig. 26-15-4 Species I Site Species II Species III I II III I I II III Ancestral sequence 1/C 4 321 C C C C T T T T T TA AA A G G I I I II III 3/A 2/T 4/C I I I II III 7 events 6 events

70. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

71. Fig. 26-16 Common ancestor of crocodilians, dinosaurs, and birds Birds Lizards and snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs

72. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles Animation: The Geologic Record Animation: The Geologic Record

73. Fig. 26-17 Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture

74. Fig. 26-17a Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs

75. Fig. 26-17b (b) Artist’s reconstruction of the dinosaur’s posture

76. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

77. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

78. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Orthologous genes are found in a single copy in the genome and are homologous between species They can diverge only after speciation occurs

79. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

80. Fig. 26-18 (b) Paralogous genes (a) Orthologous genes Ancestral gene Paralogous genes Ancestral species Speciation with divergence of gene Gene duplication and divergence Species A after many generations Species A Species B Species A Orthologous genes

81. Fig. 26-18a (a) Orthologous genes Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B Orthologous genes

82. Fig. 26-18b (b) Paralogous genes Paralogous genes Gene duplication and divergence Species A after many generations Species A

83. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

84. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

85. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

86. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Molecular clocks are calibrated against branches whose dates are known from the fossil record

87. Fig. 26-19 Divergence time (millions of years) Number of mutations 120 90 60 30 0 0

88. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

89. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

90. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

91. Fig. 26-20 Year Index of base changes between HIV sequences 1960 0.20 194019201900 0 19802000 0.15 0.10 0.05 Range Computer model of HIV

92. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

93. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 Animation: Classification Schemes

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

95. Fig. 26-21a Green nonsulfur bacteria COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur bacteria (Mitochondrion) Cyanobacteria Chlamydia Spirochetes

96. Fig. 26-21b Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA

97. Fig. 26-21c Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals Amoebas Cellular slime molds Leishmania Euglena

98. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

99. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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

100. 3 Archaea Bacteria Eukarya Billions of years ago 4 21 0 What might this indicate about the influence of bacteria in our gut?

101. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 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 Is the Tree of Life Really a Ring?

102. Fig. 26-23 Archaea Bacteria Eukarya

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

104. Fig. 26-UN3 F Polyphyletic group Monophyletic group Paraphyletic group E D C B A G AA BB C C D D E E F F GG

105. Fig. 26-UN4 Lizard Salamander Goat Human

106. Fig. 26-UN5

107. Fig. 26-UN6

108. Fig. 26-UN7

109. Fig. 26-UN8

110. Fig. 26-UN9

111. Fig. 26-UN10

112. Fig. 26-UN10a

113. Fig. 26-UN10b

114. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings You should now be able to: 1.Explain the justification for taxonomy based on a PhyloCode 2.Explain the importance of distinguishing between homology and analogy 3.Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes

115. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings 4.Define horizontal gene transfer and explain how it complicates phylogenetic trees 5.Explain molecular clocks and discuss their limitations