1. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Organizing groups of organisms into clades using phylogenetics (Using characteristics that indicate common ancestry to show evolutionary relationships)

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

3. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Taxonomy is the ordered division and naming of organisms

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

5. 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)

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

7. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia ArchaeaDomain: Eukarya Bacteria

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

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

10. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Systematists depict evolutionary relationships in branching phylogenetic trees

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

12. 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

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

14. 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

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

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

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

18. 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

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

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

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

22. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax

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

24. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms

25. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

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

27. Fig. 26-7

28. 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

29. 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

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

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

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

33. Fig. 26-8b 3 4

34. 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

35. Fig. 26-9

36. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Once homologous characters have been identified, they can be used to infer a phylogeny

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

38. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

39. 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

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

41. 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

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

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

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

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

46. 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

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

48. 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

49. Fig. 26-11a TAXA Lancelet (outgroup) 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

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

51. 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

52. 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

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

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

55. 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

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

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

58. 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

59. 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

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

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

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

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

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

65. 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

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

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

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

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

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

71. 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

72. 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

73. 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

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

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

76. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

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

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

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

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

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

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

83. 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

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

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

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

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

88. 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

89. Fig. 26-22 3 Archaea Bacteria Eukarya Billions of years ago 4 21 0

90. 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?

91. Fig. 26-23 Archaea Bacteria Eukarya

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

93. 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

94. Fig. 26-UN4 Lizard Salamander Goat Human

95. Fig. 26-UN5

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

97. 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