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Chapter 26 Presentation

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  • Figure 26.1 What is this organism?
  • Figure 26.2 An unexpected family tree
  • Figure 26.3 Hierarchical classification
  • Figure 26.3 Hierarchical classification
  • Figure 26.3 Hierarchical classification
  • Figure 26.4 The connection between classification and phylogeny
  • Figure 26.5 How to read a phylogenetic tree
  • Figure 26.6 What is the species identity of food being sold as whale meat?
  • Figure 26.6 What is the species identity of food being sold as whale meat?
  • Figure 26.6 What is the species identity of food being sold as whale meat?
  • Figure 26.6 What is the species identity of food being sold as whale meat?
  • Figure 26.7 Convergent evolution of analogous burrowing characteristics
  • Figure 26.8 Aligning segments of DNA
  • Figure 26.8 Aligning segments of DNA
  • Figure 26.8 Aligning segments of DNA
  • Figure 26.9 A molecular homoplasy
  • Figure 26.10 Monophyletic, paraphyletic, and polyphyletic groups
  • Figure 26.10a Monophyletic, paraphyletic, and polyphyletic groups
  • Figure 26.10b Monophyletic, paraphyletic, and polyphyletic groups
  • Figure 26.10c Monophyletic, paraphyletic, and polyphyletic groups
  • Figure 26.11 Constructing a phylogenetic tree
  • Figure 26.11 Constructing a phylogenetic tree
  • Figure 26.11 Constructing a phylogenetic tree
  • Figure 26.12 Branch lengths can indicate relative amounts of genetic change
  • Figure 26.13 Branch lengths can indicate time
  • Figure 26.14 Trees with different likelihoods
  • Figure 26.14 Trees with different likelihoods
  • Figure 26.14 Trees with different likelihoods
  • Figure 26.15 Applying parsimony to a problem in molecular systematics
  • Figure 26.15 Applying parsimony to a problem in molecular systematics
  • Figure 26.15 Applying parsimony to a problem in molecular systematics
  • Figure 26.15 Applying parsimony to a problem in molecular systematics
  • lFigure 26.16 A phylogenetic tree of birds and their close relatives
  • Figure 26.17 Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
  • Figure 26.17 Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
  • Figure 26.17 Fossils support a phylogenetic prediction: Dinosaurs built nests and brooded their eggs
  • Figure 26.18 How two types of homologous genes originate
  • Figure 26.18 How two types of homologous genes originate
  • Figure 26.18 How two types of homologous genes originate
  • Figure 26.19 A molecular clock for mammals
  • Figure 26.20 Dating the origin of HIV-1 M with a molecular clock
  • Figure 26.21 The three domains of life
  • Figure 26.21 The three domains of life
  • Figure 26.21 The three domains of life
  • Figure 26.21 The three domains of life
  • Figure 26.22 The role of horizontal gene transfer in the history of life
  • Figure 26.23 A ring of life
  • Transcript

    • 1. Chapter 26 Phylogeny and the Tree of Life
    • 2. Fig. 26-1
    • 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
    • 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. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: Eukarya Bacteria
    • 10. Fig. 26-3a Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: Eukarya Bacteria
    • 11. Fig. 26-3b Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora
    • 12. Linking Classification and Phylogeny
      • Systematists depict evolutionary relationships in branching phylogenetic trees
    • 13. Fig. 26-4 Species Canis lupus Pantherapardus Taxidea taxus Lutra lutra Canis latrans Order Family Genus Carnivora Felidae Mustelidae Canidae Canis Lutra Taxidea Panthera
    • 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. 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
    • 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 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.
      • Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax
    • 25. Fig. 26-UN1 A B A A B B C C C D D D (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
    • 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. Fig. 26-8 Deletion Insertion 1 2 3 4
    • 34. Fig. 26-8a Deletion Insertion 1 2
    • 35. Fig. 26-8b 3 4
    • 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
    • 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. Fig. 26-10 A A A B B B C C C D D D E E E F F F G G G Group III Group II Group I (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group
    • 42. Fig. 26-10a A B C D E F G Group I (a) Monophyletic group (clade)
    • 43.
      • 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.
      • 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. 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. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
    • 51. 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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 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.
      • 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. Fig. 26-12 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse
    • 57.
      • In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record
    • 58. Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present 65.5 MESOZOIC 251 Millions of years ago PALEOZOIC 542
    • 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. Fig. 26-14 Human 15% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees 15% 15% 5% 5% 10% 25% 20% 40% 40% 30% 0 0 0 (a) Percentage differences between sequences Human Mushroom Mushroom Tulip Tulip
    • 62. Fig. 26-14a Human 40% 40% 30% 0 0 0 (a) Percentage differences between sequences Human Mushroom Mushroom Tulip Tulip
    • 63. Fig. 26-14b 15% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees 15% 15% 5% 5% 10% 25% 20%
    • 64.
      • Computer programs are used to search for trees that are parsimonious and likely
    • 65. Fig. 26-15-1 Species I Three phylogenetic hypotheses: Species II Species III I II III I I II II III III
    • 66. Fig. 26-15-2 Species I Site Species II Species III I II III I I II II III III Ancestral sequence 1/C 1/C 1/C 1/C 1/C 4 3 2 1 C C C C T T T T T T A A A A G G
    • 67. Fig. 26-15-3 Species I Site Species II Species III I II III I I II II III III Ancestral sequence 1/C 1/C 1/C 1/C 1/C 4 3 2 1 C C C C T T T T T T A A A A G G I I I II II II III III III 3/A 3/A 3/A 3/A 3/A 2/T 2/T 2/T 2/T 2/T 4/C 4/C 4/C 4/C 4/C
    • 68. Fig. 26-15-4 Species I Site Species II Species III I II III I I II II III III Ancestral sequence 1/C 1/C 1/C 1/C 1/C 4 3 2 1 C C C C T T T T T T A A A A G G I I I II II II III III III 3/A 3/A 3/A 3/A 3/A 2/T 2/T 2/T 2/T 2/T 4/C 4/C 4/C 4/C 4/C I I I II II II III III III 7 events 7 events 6 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. Fig. 26-16 Common ancestor of crocodilians, dinosaurs, and birds Birds Lizards and snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs
    • 71.
      • This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles
      Animation: The Geologic Record
    • 72. Fig. 26-17 Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur’s posture
    • 73. Fig. 26-17a Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs
    • 74. Fig. 26-17b (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. 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
    • 80. Fig. 26-18a (a) Orthologous genes Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B Orthologous genes
    • 81. Fig. 26-18b (b) Paralogous genes Paralogous genes Gene duplication and divergence Species A after many generations Species A
    • 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. Fig. 26-19 Divergence time (millions of years) Number of mutations 120 90 90 60 60 30 30 0 0
    • 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. Fig. 26-20 Year Index of base changes between HIV sequences 1960 0.20 1940 1920 1900 0 1980 2000 0.15 0.10 0.05 Range Computer model of HIV
    • 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. 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
    • 94. Fig. 26-21a Green nonsulfur bacteria COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur bacteria (Mitochondrion) Cyanobacteria Chlamydia Spirochetes
    • 95. Fig. 26-21b Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA
    • 96. Fig. 26-21c Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals Amoebas Cellular slime molds Leishmania Euglena
    • 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. Fig. 26-22 3 Archaea Bacteria Eukarya Billions of years ago 4 2 1 0
    • 100.
      • 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?
    • 101. Fig. 26-23 Archaea Bacteria Eukarya
    • 102. Fig. 26-UN2 Taxon F Sister taxa Node Polytomy Most recent common ancestor Taxon E Taxon D Taxon C Taxon B Taxon A
    • 103. Fig. 26-UN3 F Polyphyletic group Monophyletic group Paraphyletic group E D C B A G A A B B C C D D E E F F G G
    • 104. Fig. 26-UN4 Lizard Salamander 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