Chapter 26 Phylogeny and the Tree of Life
Fig. 26-1
Overview: Investigating the Tree of Life <ul><li>Phylogeny  is the evolutionary history of a species or group of related s...
Fig. 26-2
Concept 26.1: Phylogenies show evolutionary relationships <ul><li>Taxonomy  is the ordered division and naming of organism...
Binomial Nomenclature <ul><li>In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances <...
<ul><li>The two-part scientific name of a species is called a  binomial </li></ul><ul><li>The first part of the name is th...
Hierarchical Classification <ul><li>Linnaeus introduced a system for grouping species in increasingly broad categories </l...
Fig. 26-3 Species: Panthera pardus Genus:  Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata King...
Fig. 26-3a Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: Eukarya Bacteria
Fig. 26-3b Species: Panthera pardus Genus:  Panthera Family: Felidae Order: Carnivora
Linking Classification and Phylogeny <ul><li>Systematists depict evolutionary relationships in branching  phylogenetic tre...
Fig. 26-4 Species Canis lupus Pantherapardus Taxidea taxus Lutra lutra Canis latrans Order Family Genus Carnivora Felidae ...
<ul><li>Linnaean classification and phylogeny can differ from each other </li></ul><ul><li>Systematists have proposed the ...
<ul><li>A phylogenetic tree represents a hypothesis about evolutionary relationships </li></ul><ul><li>Each  branch point ...
<ul><li>A  rooted  tree includes a branch to represent the last common ancestor of all taxa in the tree </li></ul><ul><li>...
Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Polytomy Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C T...
What We Can and Cannot Learn from Phylogenetic Trees <ul><li>Phylogenetic trees do show patterns of descent </li></ul><ul>...
Applying Phylogenies <ul><li>Phylogeny provides important information about similar characteristics in closely related spe...
Fig. 26-6 Fin (Mediterranean) Fin (Iceland) RESULTS Unknown #10, 11, 12 Unknown #13 Blue (North Pacific) Blue (North Atlan...
Fig. 26-6a Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 RESULTS
Fig. 26-6b Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific)
Fig. 26-6c Fin (Mediterranean) Fin (Iceland) Unknown #13 Unknown #10, 11, 12
<ul><li>Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax </li></ul>
Fig. 26-UN1 A B A A B B C C C D D D (a) (b) (c)
Concept 26.2: Phylogenies are inferred from morphological and molecular data <ul><li>To infer phylogenies, systematists ga...
Morphological and Molecular Homologies <ul><li>Organisms with similar morphologies or DNA sequences are likely to be more ...
Sorting Homology from Analogy <ul><li>When constructing a phylogeny, systematists need to distinguish whether a similarity...
Fig. 26-7
<ul><li>Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous)...
<ul><li>Bat and bird wings are homologous as forelimbs, but analogous as functional wings </li></ul><ul><li>Analogous stru...
Evaluating Molecular Homologies <ul><li>Systematists use computer programs and mathematical tools when analyzing comparabl...
Fig. 26-8 Deletion Insertion 1 2 3 4
Fig. 26-8a Deletion Insertion 1 2
Fig. 26-8b 3 4
<ul><li>It is also important to distinguish homology from analogy in molecular similarities </li></ul><ul><li>Mathematical...
Fig. 26-9
Concept 26.3: Shared characters are used to construct phylogenetic trees <ul><li>Once homologous characters have been iden...
Cladistics <ul><li>Cladistics  groups organisms by common descent </li></ul><ul><li>A  clade  is a group of species that i...
<ul><li>A valid clade is  monophyletic , signifying that it consists of the ancestor species and all its descendants </li>...
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) Para...
Fig. 26-10a A B C D E F G Group  I (a) Monophyletic group (clade)
<ul><li>A  paraphyletic  grouping consists of an ancestral species and some, but not all, of the descendants </li></ul>
Fig. 26-10b A B C D E F G Group  II (b) Paraphyletic group
<ul><li>A  polyphyletic  grouping consists of various species that lack a common ancestor </li></ul>
Fig. 26-10c A B C D E F G Group  III (c) Polyphyletic group
Shared Ancestral and Shared Derived Characters <ul><li>In comparison with its ancestor, an organism has both shared and di...
<ul><li>A  shared ancestral character  is a character that originated in an ancestor of the taxon </li></ul><ul><li>A  sha...
Inferring Phylogenies Using Derived Characters <ul><li>When inferring evolutionary relationships, it is useful to know in ...
Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four wa...
Fig. 26-11a TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four w...
Fig. 26-11b Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turt...
<ul><li>An  outgroup  is a species or group of species that is closely related to the  ingroup , the various species being...
<ul><li>Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups ...
Phylogenetic Trees with Proportional Branch Lengths <ul><li>In some trees, the length of a branch can reflect the number o...
Fig. 26-12 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse
<ul><li>In other trees, branch length can represent chronological time, and branching points can be determined from the fo...
Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present 65.5 MESOZOIC 251 Millions of years ago...
Maximum Parsimony and Maximum Likelihood <ul><li>Systematists can never be sure of finding the best tree in a large data s...
<ul><li>Maximum parsimony  assumes that the tree that requires the fewest evolutionary events (appearances of shared deriv...
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...
Fig. 26-14a Human 40% 40% 30% 0 0 0 (a) Percentage differences between sequences Human Mushroom Mushroom Tulip Tulip
Fig. 26-14b 15% Tree 1: More likely Tree 2: Less likely (b) Comparison of possible trees 15% 15% 5% 5% 10% 25% 20%
<ul><li>Computer programs are used to search for trees that are parsimonious and likely </li></ul>
Fig. 26-15-1 Species  I Three phylogenetic hypotheses: Species  II Species  III I II III I I II II III III
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 ...
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 ...
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 ...
Phylogenetic Trees as Hypotheses <ul><li>The best hypotheses for phylogenetic trees fit the most data: morphological, mole...
Fig. 26-16 Common ancestor of crocodilians, dinosaurs, and birds Birds Lizards and snakes Crocodilians Ornithischian dinos...
<ul><li>This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles </li></ul>Animat...
Fig. 26-17 Eggs Front limb Hind limb (a) Fossil remains of  Oviraptor and eggs (b) Artist’s reconstruction of the dinosaur...
Fig. 26-17a Eggs Front limb Hind limb (a) Fossil remains of  Oviraptor and eggs
Fig. 26-17b (b) Artist’s reconstruction of the dinosaur’s posture
Concept 26.4: An organism’s evolutionary history is documented in its genome <ul><li>Comparing nucleic acids or other mole...
Gene Duplications and Gene Families <ul><li>Gene duplication increases the number of genes in the genome, providing more o...
<ul><li>Orthologous genes  are found in a single copy in the genome and are homologous between species </li></ul><ul><li>T...
<ul><li>Paralogous genes  result from gene duplication, so are found in more than one copy in the genome </li></ul><ul><li...
Fig. 26-18 (b) Paralogous genes (a) Orthologous genes Ancestral gene Paralogous genes Ancestral species Speciation with di...
Fig. 26-18a (a) Orthologous genes Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B ...
Fig. 26-18b (b) Paralogous genes Paralogous genes Gene duplication and divergence Species A after many generations Species A
Genome Evolution <ul><li>Orthologous genes are widespread and extend across many widely varied species </li></ul><ul><li>G...
Concept 26.5: Molecular clocks help track evolutionary time <ul><li>To extend molecular phylogenies beyond the fossil reco...
Molecular Clocks <ul><li>A  molecular clock  uses constant rates of evolution in some genes to estimate the absolute time ...
<ul><li>Molecular clocks are calibrated against branches whose dates are known from the fossil record </li></ul>
Fig. 26-19 Divergence time (millions of years) Number of mutations 120 90 90 60 60 30 30 0 0
Neutral Theory <ul><li>Neutral theory  states that much evolutionary change in genes and proteins has no effect on fitness...
Difficulties with Molecular Clocks <ul><li>The molecular clock does not run as smoothly as neutral theory predicts </li></...
Applying a Molecular Clock: The Origin of HIV <ul><li>Phylogenetic analysis shows that HIV is descended from viruses that ...
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 Comp...
Concept 26.6: New information continues to revise our understanding of the tree of life <ul><li>Recently, we have gained i...
From Two Kingdoms to Three Domains <ul><li>Early taxonomists classified all species as either plants or animals </li></ul>...
Fig. 26-21 Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals Am...
Fig. 26-21a Green nonsulfur bacteria COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur ...
Fig. 26-21b Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA
Fig. 26-21c Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals A...
A Simple Tree of All Life <ul><li>The tree of life suggests that eukaryotes and archaea are more closely related to each o...
<ul><li>There have been substantial interchanges of genes between organisms in different domains </li></ul><ul><li>Horizon...
Fig. 26-22 3 Archaea Bacteria Eukarya Billions of years ago 4 2 1 0
<ul><li>Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean </li></ul><ul>...
Fig. 26-23 Archaea Bacteria Eukarya
Fig. 26-UN2 Taxon F Sister taxa Node Polytomy Most recent common ancestor Taxon E Taxon D Taxon C Taxon B Taxon A
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
Fig. 26-UN4 Lizard Salamander Goat Human
Fig. 26-UN5
Fig. 26-UN6
Fig. 26-UN7
Fig. 26-UN8
Fig. 26-UN9
Fig. 26-UN10
Fig. 26-UN10a
Fig. 26-UN10b
You should now be able to: <ul><li>Explain the justification for taxonomy based on a PhyloCode </li></ul><ul><li>Explain t...
<ul><li>Define horizontal gene transfer and explain how it complicates phylogenetic trees </li></ul><ul><li>Explain molecu...
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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
  • Chapter 26 Presentation

    1. 1. Chapter 26 Phylogeny and the Tree of Life
    2. 2. Fig. 26-1
    3. 3. Overview: Investigating the Tree of Life <ul><li>Phylogeny is the evolutionary history of a species or group of related species </li></ul><ul><li>The discipline of systematics classifies organisms and determines their evolutionary relationships </li></ul><ul><li>Systematists use fossil, molecular, and genetic data to infer evolutionary relationships </li></ul>
    4. 4. Fig. 26-2
    5. 5. Concept 26.1: Phylogenies show evolutionary relationships <ul><li>Taxonomy is the ordered division and naming of organisms </li></ul>
    6. 6. Binomial Nomenclature <ul><li>In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances </li></ul><ul><li>Two key features of his system remain useful today: two-part names for species and hierarchical classification </li></ul>
    7. 7. <ul><li>The two-part scientific name of a species is called a binomial </li></ul><ul><li>The first part of the name is the genus </li></ul><ul><li>The second part, called the specific epithet, is unique for each species within the genus </li></ul><ul><li>The first letter of the genus is capitalized, and the entire species name is italicized </li></ul><ul><li>Both parts together name the species (not the specific epithet alone) </li></ul>
    8. 8. Hierarchical Classification <ul><li>Linnaeus introduced a system for grouping species in increasingly broad categories </li></ul><ul><li>The taxonomic groups from broad to narrow are domain , kingdom , phylum , class , order , family , genus , and species </li></ul><ul><li>A taxonomic unit at any level of hierarchy is called a taxon </li></ul>
    9. 9. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: Eukarya Bacteria
    10. 10. Fig. 26-3a Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: Eukarya Bacteria
    11. 11. Fig. 26-3b Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora
    12. 12. Linking Classification and Phylogeny <ul><li>Systematists depict evolutionary relationships in branching phylogenetic trees </li></ul>
    13. 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. 14. <ul><li>Linnaean classification and phylogeny can differ from each other </li></ul><ul><li>Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents </li></ul>
    15. 15. <ul><li>A phylogenetic tree represents a hypothesis about evolutionary relationships </li></ul><ul><li>Each branch point represents the divergence of two species </li></ul><ul><li>Sister taxa are groups that share an immediate common ancestor </li></ul>
    16. 16. <ul><li>A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree </li></ul><ul><li>A polytomy is a branch from which more than two groups emerge </li></ul>
    17. 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. 18. What We Can and Cannot Learn from Phylogenetic Trees <ul><li>Phylogenetic trees do show patterns of descent </li></ul><ul><li>Phylogenetic trees do not indicate when species evolved or how much genetic change occurred in a lineage </li></ul><ul><li>It shouldn’t be assumed that a taxon evolved from the taxon next to it </li></ul>
    19. 19. Applying Phylogenies <ul><li>Phylogeny provides important information about similar characteristics in closely related species </li></ul><ul><li>A phylogeny was used to identify the species of whale from which “whale meat” originated </li></ul>
    20. 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. 21. Fig. 26-6a Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 RESULTS
    22. 22. Fig. 26-6b Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific)
    23. 23. Fig. 26-6c Fin (Mediterranean) Fin (Iceland) Unknown #13 Unknown #10, 11, 12
    24. 24. <ul><li>Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax </li></ul>
    25. 25. Fig. 26-UN1 A B A A B B C C C D D D (a) (b) (c)
    26. 26. Concept 26.2: Phylogenies are inferred from morphological and molecular data <ul><li>To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms </li></ul>
    27. 27. Morphological and Molecular Homologies <ul><li>Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences </li></ul>
    28. 28. Sorting Homology from Analogy <ul><li>When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy </li></ul><ul><li>Homology is similarity due to shared ancestry </li></ul><ul><li>Analogy is similarity due to convergent evolution </li></ul>
    29. 29. Fig. 26-7
    30. 30. <ul><li>Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages </li></ul>
    31. 31. <ul><li>Bat and bird wings are homologous as forelimbs, but analogous as functional wings </li></ul><ul><li>Analogous structures or molecular sequences that evolved independently are also called homoplasies </li></ul><ul><li>Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity </li></ul><ul><li>The more complex two similar structures are, the more likely it is that they are homologous </li></ul>
    32. 32. Evaluating Molecular Homologies <ul><li>Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms </li></ul>
    33. 33. Fig. 26-8 Deletion Insertion 1 2 3 4
    34. 34. Fig. 26-8a Deletion Insertion 1 2
    35. 35. Fig. 26-8b 3 4
    36. 36. <ul><li>It is also important to distinguish homology from analogy in molecular similarities </li></ul><ul><li>Mathematical tools help to identify molecular homoplasies, or coincidences </li></ul><ul><li>Molecular systematics uses DNA and other molecular data to determine evolutionary relationships </li></ul>
    37. 37. Fig. 26-9
    38. 38. Concept 26.3: Shared characters are used to construct phylogenetic trees <ul><li>Once homologous characters have been identified, they can be used to infer a phylogeny </li></ul>
    39. 39. Cladistics <ul><li>Cladistics groups organisms by common descent </li></ul><ul><li>A clade is a group of species that includes an ancestral species and all its descendants </li></ul><ul><li>Clades can be nested in larger clades, but not all groupings of organisms qualify as clades </li></ul>
    40. 40. <ul><li>A valid clade is monophyletic , signifying that it consists of the ancestor species and all its descendants </li></ul>
    41. 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. 42. Fig. 26-10a A B C D E F G Group I (a) Monophyletic group (clade)
    43. 43. <ul><li>A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants </li></ul>
    44. 44. Fig. 26-10b A B C D E F G Group II (b) Paraphyletic group
    45. 45. <ul><li>A polyphyletic grouping consists of various species that lack a common ancestor </li></ul>
    46. 46. Fig. 26-10c A B C D E F G Group III (c) Polyphyletic group
    47. 47. Shared Ancestral and Shared Derived Characters <ul><li>In comparison with its ancestor, an organism has both shared and different characteristics </li></ul>
    48. 48. <ul><li>A shared ancestral character is a character that originated in an ancestor of the taxon </li></ul><ul><li>A shared derived character is an evolutionary novelty unique to a particular clade </li></ul><ul><li>A character can be both ancestral and derived, depending on the context </li></ul>
    49. 49. Inferring Phylogenies Using Derived Characters <ul><li>When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared </li></ul>
    50. 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. 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. 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. 53. <ul><li>An outgroup is a species or group of species that is closely related to the ingroup , the various species being studied </li></ul><ul><li>Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics </li></ul>
    54. 54. <ul><li>Homologies shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor </li></ul>
    55. 55. Phylogenetic Trees with Proportional Branch Lengths <ul><li>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 </li></ul>
    56. 56. Fig. 26-12 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse
    57. 57. <ul><li>In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record </li></ul>
    58. 58. Fig. 26-13 Drosophila Lancelet Zebrafish Frog Human Chicken Mouse CENOZOIC Present 65.5 MESOZOIC 251 Millions of years ago PALEOZOIC 542
    59. 59. Maximum Parsimony and Maximum Likelihood <ul><li>Systematists can never be sure of finding the best tree in a large data set </li></ul><ul><li>They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood </li></ul>
    60. 60. <ul><li>Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely </li></ul><ul><li>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 </li></ul>
    61. 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. 62. Fig. 26-14a Human 40% 40% 30% 0 0 0 (a) Percentage differences between sequences Human Mushroom Mushroom Tulip Tulip
    63. 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. 64. <ul><li>Computer programs are used to search for trees that are parsimonious and likely </li></ul>
    65. 65. Fig. 26-15-1 Species I Three phylogenetic hypotheses: Species II Species III I II III I I II II III III
    66. 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. 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. 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. 69. Phylogenetic Trees as Hypotheses <ul><li>The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil </li></ul><ul><li>Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents </li></ul>
    70. 70. Fig. 26-16 Common ancestor of crocodilians, dinosaurs, and birds Birds Lizards and snakes Crocodilians Ornithischian dinosaurs Saurischian dinosaurs
    71. 71. <ul><li>This has been applied to infer features of dinosaurs from their descendents: birds and crocodiles </li></ul>Animation: The Geologic Record
    72. 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. 73. Fig. 26-17a Eggs Front limb Hind limb (a) Fossil remains of Oviraptor and eggs
    74. 74. Fig. 26-17b (b) Artist’s reconstruction of the dinosaur’s posture
    75. 75. Concept 26.4: An organism’s evolutionary history is documented in its genome <ul><li>Comparing nucleic acids or other molecules to infer relatedness is a valuable tool for tracing organisms’ evolutionary history </li></ul><ul><li>DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago </li></ul><ul><li>mtDNA evolves rapidly and can be used to explore recent evolutionary events </li></ul>
    76. 76. Gene Duplications and Gene Families <ul><li>Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes </li></ul><ul><li>Like homologous genes, duplicated genes can be traced to a common ancestor </li></ul>
    77. 77. <ul><li>Orthologous genes are found in a single copy in the genome and are homologous between species </li></ul><ul><li>They can diverge only after speciation occurs </li></ul>
    78. 78. <ul><li>Paralogous genes result from gene duplication, so are found in more than one copy in the genome </li></ul><ul><li>They can diverge within the clade that carries them and often evolve new functions </li></ul>
    79. 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. 80. Fig. 26-18a (a) Orthologous genes Ancestral gene Ancestral species Speciation with divergence of gene Species A Species B Orthologous genes
    81. 81. Fig. 26-18b (b) Paralogous genes Paralogous genes Gene duplication and divergence Species A after many generations Species A
    82. 82. Genome Evolution <ul><li>Orthologous genes are widespread and extend across many widely varied species </li></ul><ul><li>Gene number and the complexity of an organism are not strongly linked </li></ul><ul><li>Genes in complex organisms appear to be very versatile and each gene can perform many functions </li></ul>
    83. 83. Concept 26.5: Molecular clocks help track evolutionary time <ul><li>To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time </li></ul>
    84. 84. Molecular Clocks <ul><li>A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change </li></ul><ul><li>In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor </li></ul><ul><li>In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated </li></ul>
    85. 85. <ul><li>Molecular clocks are calibrated against branches whose dates are known from the fossil record </li></ul>
    86. 86. Fig. 26-19 Divergence time (millions of years) Number of mutations 120 90 90 60 60 30 30 0 0
    87. 87. Neutral Theory <ul><li>Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by Darwinian selection </li></ul><ul><li>It states that the rate of molecular change in these genes and proteins should be regular like a clock </li></ul>
    88. 88. Difficulties with Molecular Clocks <ul><li>The molecular clock does not run as smoothly as neutral theory predicts </li></ul><ul><li>Irregularities result from natural selection in which some DNA changes are favored over others </li></ul><ul><li>Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty </li></ul><ul><li>The use of multiple genes may improve estimates </li></ul>
    89. 89. Applying a Molecular Clock: The Origin of HIV <ul><li>Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates </li></ul><ul><li>Comparison of HIV samples throughout the epidemic shows that the virus evolved in a very clocklike way </li></ul><ul><li>Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s </li></ul>
    90. 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. 91. Concept 26.6: New information continues to revise our understanding of the tree of life <ul><li>Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics </li></ul>
    92. 92. From Two Kingdoms to Three Domains <ul><li>Early taxonomists classified all species as either plants or animals </li></ul><ul><li>Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia </li></ul><ul><li>More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya </li></ul><ul><li>The three-domain system is supported by data from many sequenced genomes </li></ul>Animation: Classification Schemes
    93. 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. 94. Fig. 26-21a Green nonsulfur bacteria COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur bacteria (Mitochondrion) Cyanobacteria Chlamydia Spirochetes
    95. 95. Fig. 26-21b Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA
    96. 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. 97. A Simple Tree of All Life <ul><li>The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria </li></ul><ul><li>The tree of life is based largely on rRNA genes, as these have evolved slowly </li></ul>
    98. 98. <ul><li>There have been substantial interchanges of genes between organisms in different domains </li></ul><ul><li>Horizontal gene transfer is the movement of genes from one genome to another </li></ul><ul><li>Horizontal gene transfer complicates efforts to build a tree of life </li></ul>
    99. 99. Fig. 26-22 3 Archaea Bacteria Eukarya Billions of years ago 4 2 1 0
    100. 100. <ul><li>Some researchers suggest that eukaryotes arose as an endosymbiosis between a bacterium and archaean </li></ul><ul><li>If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life </li></ul>Is the Tree of Life Really a Ring?
    101. 101. Fig. 26-23 Archaea Bacteria Eukarya
    102. 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. 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. 104. Fig. 26-UN4 Lizard Salamander Goat Human
    105. 105. Fig. 26-UN5
    106. 106. Fig. 26-UN6
    107. 107. Fig. 26-UN7
    108. 108. Fig. 26-UN8
    109. 109. Fig. 26-UN9
    110. 110. Fig. 26-UN10
    111. 111. Fig. 26-UN10a
    112. 112. Fig. 26-UN10b
    113. 113. You should now be able to: <ul><li>Explain the justification for taxonomy based on a PhyloCode </li></ul><ul><li>Explain the importance of distinguishing between homology and analogy </li></ul><ul><li>Distinguish between the following terms: monophyletic, paraphyletic, and polyphyletic groups; shared ancestral and shared derived characters; orthologous and paralogous genes </li></ul>
    114. 114. <ul><li>Define horizontal gene transfer and explain how it complicates phylogenetic trees </li></ul><ul><li>Explain molecular clocks and discuss their limitations </li></ul>
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