Chapter 3 -- What the Rocks Say

  1. Introduction
    1. Evidence for Evolution from mj farabee Maracopa
    2. Evolution from PBS
    3. Evidence Supporting Biological Evolution from the National Academy of Sciences
    4. Evolution: Converging Lines of Evidence 
    5. Evidence for Evolution from Talk Origins
      1. examples
  2. Direct observation of change
    1. Vestigial Organs remnants of once useful structures
      1. The brown kiwi, a flightless bird, has tiny, useless wings.
      2. Rudimentary hindlimb in boas or whales. [Fig. 1.23]
      3. human appendix;
      4. Humans have a rudimentary tailbone, called the coccyx [fig. 4.27]
      5. Humans have a muscle, the arrector pili, at the base of each hair follicle. When it contracts, producing a goosebump, the hair stands up.  If we were hairy, like this chimpanzee, then contraction of our arrector pili muscles would increase the loft of our fur to keep us warm, or to make us look more intimidating.
      6. blind cave salamanders
      7. Developmental vestigial traits Adult chickens have three digits in their wings and four in their feet. But during development, an extra digit appears for a short time in the "hand" and foot  
      8. Rudimentary organs Fitch--NYU




  1. Archbishop James Ussher (1581-1656) and a biblical chronology
  2. Charles Darwin
    1. uniformitarianism: slow changes over immense stretches of time
    2. Lord Kelvin (William Thompson 1824-1907)
      1. Earth was no more than 20 million years old based on heat loss of the Earth (Fig. 3.2)
      2. Did not take radioactivity into account
    3. The Geologic Time Scale [See inside front and back covers], figure to right from Wikipedia
      1. relative dating
      2. geologic time
      3. Unraveling Geologic Time from Paul Olsen's excellent WebPages for his dinosaur class
      4. Geologic Time Scale from the UCMP
      5. Geologic Time from the USGS
    4. relative ages
      1. stratigraphy
      2. Principle of Fossil Succession:  William Smith and Georges Cuvier
      3. Index Fossils
      4. A relative dating activity from the UCMP
    5. evolution is a time dependent process, special creation is not
    6. Radiometric Dating
      1. a basic introduction by Pamela Gore
      2. radioactive decay [Box 3.1] is an independent clock
    7. the earth is 4.6 billion years old
    8. First possible life 3.8 billion years ago
    9. Stromatolites (cyanobacterial mats) 3.4 billion years ago (Fig. 3.1)1.
    10. Transition to eucaryotic life began at least 2.1 billion years ago
    11. Ediacaran fauna (Fig. 3.20)
      1. Diverse and unique animals dominated the oceans from 575 - 535 mya
    12. Cambrian
      1. Burgess Shale (Fig. 3.20)
      2. Chordates emerged during early Cambrian(515 mya); Jawed fish by 440 mya (Fig 3.21)
    13. Oldest fossils of tetrapods date to 370 mya (Figs. 3.24-3.25)
    14. Oldest amniotes date to 340 mya
    15. Teleost fish (most ray-finned fish): Triassic, 240 Ma
    16. Birds: Jurassic, 150 Ma
    17. Flowering plants: early Cretaceous,120 million years ago
    18. Evolution of Mammals
      1. Pelycosaur synapsids emerged around 300 mya (Fig 3.26)
      2. First mammals emerged 150 mya
      3. Mammals diversified after dinosaurs went extinct (~65 mya)
      4. Whales, bats, and primates all emerged around 50 mya
      5. Oldest hominins ~7 mya


4.1 Tree Thinking p. 95

  • Phylogenies are hypotheses that are constructed using shared, derived characters.
  • These characters can be morphological or genetic.
  1. Reading a Tree
    1. species are related by descent from a common ancestor.
    2. Evolutionary trees describe histories of descent with modification
    3. Darwin's hypothetical tree (Figure to right), showing a phylogeny with tips, branches, and nodes, is the only figure in The Origin of Species
    4. Cladograms show the relationships of taxa
      1.  Journey into the world of phylogenetic systematics from the UCMP




4.4 Fossils, Phylogeny, and the Timing of Evolution p. 106

  1. Incorporating fossils into phylogenies makes it possible to discover things that we would not know if we studied only the taxa alive today
  2. The Law of Succession
    1. Lyell saw a 'law of succession' with mammals being replaced by their own kind on each continent
    2. Darwin noted the similarities between the contemporary pygmy armadillo (Zaedyus pichyi)  and the fossil glyptodont of Argentina.
    3. Richard Owen confirmed a pattern first recognized by William Clift when Owen identified the extinct Australian mammal Diprotodon as a marsupial similar to the wombats that live in Australia today

Transitional Forms

From Fins to Limbs: Homology through Time p. 108

  1. The colonization of land marks an important evolutionary transition now documented in the fossil record.
  2. Tiktaalik (Figs. 4.2, 4.201 4.22)

Evolution as Tinkering  p. 114

  1. Adaptations do not appear magically in the fossil record
  2. existing components can be modified and co-opted for new functions
  3. selection can lead to new characteristics by changing functions of preexisting traits, genes, etc.
  4. preadaptations, exaptiion
  5. The mammalian middle ear (Figs. 4.25-27)

 Feathered Dinosaurs Take Flight p. 118

  • Feathers are not unique to birds, and they did not evolve for flight.
    1. The dinosaur-bird transition (Fig. 4.29)
      1. Archaeopteryx (Fig 4.28), a bird with modern feathers and a dinosaur-like skeleton.
      2. Sinosauropteryx prima, a dinosaur with bristly structures on its neck, back, flanks, and tail that many paleontologists believe are down-like feather
      3. Caudipteryx zoui, a dinosaur with elongated feathers on its arms and tail.
      4.  Anchiornis huxleyi, (Fig. 3.8)
      5.  Microraptor gui, a dromaeosaur with flight feathers on all four limbs--that is, a four-winged dinosaur.
  • Tiktaalik
    Tiktaalik in the Field Museum, Chicago. Image from Wikipedia

    A New Ape  (Chapter 17)

    • Humans have a grand history
    • a history being discovered in depth as more and more fossil hominids are unearthed.


    1. Darwin proposed that humans most closely related to African apes 
      1. Fossil record should document transition to to unique human traits
        1. Bipedality
        2. Larger brain size
        3. Smaller canine teeth
    2. Phylogeny reveals transitions  (Fig. 17.6)
    3. Transition to bipedality  (Fig. 17.7)
      1. Appears to have evolved before larger brain
        1. Position of foramen magnum
        2. Weight bearing stance
        3. Short, stiff toes
    4. Ardipithecus (5.5-4.4 Ma), adapted to walking and arboreal life  (Fig. 17.8)

      Ardipithecus Zanclean skull.  Photo by T M Keesey
    5. Hominins became better adapted to walking upright over time
      1. Tracks made by Australopithecus afarensis  (3.6 mya)  and  Homo 1.5 Ma (Fig. 17.16)
      2. Homo erectus (Fig. 17.7)

    Freeman and Herron Chapter 20


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    review questions

    Hominin species distributed through time.  From Wikipedia



    1. Figure 20.1 Phylogeny of the apes
      1. This evolutionary tree shows the relationships among the Old World monkeys, represented by a rhesus monkey, and the apes and humans. Among the apes, the gibbons branch off first, followed by the orangutan. The evolutionary relationships among the gorilla, the two chimpanzees, and humans (triangle with question mark) were long the subject of considerable dispute
    2. Phylogeny based on anatomy
    3. Figure 20.2 Sarich and Wilson's phylogeny of the apes.
      1. Immunological distance (antibody response), showing humans and African apes diverged about 5 Ma.
    4. Figure 20.3 Possible phylogenies of humans and the African great apes
      1. The figure shows four possible resolutions of the evolutionary relationships among humans and the African great apes. All assume that the two species of chimpanzee are closest relatives. The true tree could have (a) chimpanzees and humans as closest relatives, (b) gorillas and chimpanzees as closest relatives, (c) gorillas and humans as closest relatives, or (d) a genuine simultaneous three-way split (trichotomy).
    5. Figure 20.4 Phylogeny of mitochondrial cytochrome oxidase II alleles in humans and the African great apes.  Ruvolo and colleagues estimated this tree using the maximum parsimony method.
    6. Figure 20.6 Divergence times for the apes
      1. Stauffer and colleagues estimated the dates of the common ancestors on this phylogeny by combining data from dozens of proteins used as molecular clocks. The heavy bars show +/- 1 standard error around the time estimates; the lighter bars show 95% confidence intervals.
    7. Figure 20.7 Human chromosome 2 and its homologues in chimpanzees and gorillas
      1. The banding patterns on stained chromosomes reveal that human chromosome 2 is derived from the fusion of two chromosomes that remain separate in the other great apes.
    8. Telling apes from humans Panda's Thumb
      1. Creationists are always very definite that there are absolutely, absolutely no transitional fossils between apes and humans."
      2. Here are some photos of fossil skulls, all to the same scale. Some are of humans, some of apes. Care to identify which are which?

    The Fossil Record 

    1. Figure 20.9 Sahelanthropus tchadensis
      1. This 6-7 million-year-old skull, found by a member of a team led by Michel Brunet, may represent a close relative of our common ancestor with the chimpanzees. From Wood (2002).
    2. Ardipithecus ramidus
      1. New York Times article
    3. Figure 20.10.  Gracile australopithecines, Kenyanthropus, and Ardipithecus
      1. Ardipithecus (5.5-4.4 Ma), with species Ar. kadabba and Ar. ramidus;
      2. Australopithecus (4-2 Ma), with species Au. anamensis, Au. afarensis, Au. africanus, Au. bahrelghazali, and Au. garhi;
      3. Kenyanthropus (3-2.7 Ma), with species Kenyanthropus platyops
    4. Figure 20.11 Footprints of a pair of Australopithecus afarensis

      1. These 3.6-million-year-old footprints from Laetoli, Tanzania were made by a pair of individuals who walked side-by-side through fresh ash from a volcanic eruption.
    5. Figure 20.12 Paranthropus (robust australopithecines)
      1. Paranthropus (3�1.2 Ma), with species P. aethiopicus, P. boisei, and P. robustus;
    6. Figure 20.13:  Early humans
      1. Homo habilis H. rudolfensis, H. ergaster
    7. Figure 20.14: Recent humans
      1. H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens
    8. Figure 20.15 Summary of fossil evidence on the recent ancestry of humans
      1. The vertical axis gives approximate time ranges for the species we have mentioned. Horizontally, the hominin species are grouped roughly by morphological similarity. Chimpanzees are the outgroup.
      2. Figure 20.15 from Darwiniana: Transitional Human Fossils

    9. Figure 20.16: Cladogram and phylogeny of Homo sapiens and its recent ancestors and extinct relatives
      1. A cladogram of three extant hominins (the gorilla, the common chimpanzee, and the modern human), and several extinct hominins known only from fossils.
      2. A hypothesis about the ancestor-descendant relationships implied by the cladogram in (a). The heavy green vertical bars indicate the known range of times over which each species existed, whereas the heavy green dashes represent the suspected range of times over which each species existed.
    10. Figure 20.17 Evidence of a hominin radiation
      1. Paranthropus boisei (specimen KNM-ER 406, left) and Homo ergaster (specimen KNM-ER 3733) both lived in what is now Koobi Fora, Kenya, about 1.7 million years ago. From Johanson, Edgar, and Brill (1996).
    11. Figure 20.18 Hypotheses concerning the transition from Homo ergaster/erectus to Homo sapiens
      1. The white portions of the phylogenies represent various archaic forms of Homo, including H. ergaster, H. erectus, H. heidelbergensis, and H. neanderthalensis. The colored portions represent modern H. sapiens. The small blue arrows represent gene flow. Note that specimens identified as H. heidelbergensis have been found in Europe and Africa, and specimens identified as H. neanderthalensis have been found in Europe and the Middle East.
        1. (a) The African replacement model. According to this model, modern H. sapiens evolved in Africa and then migrated to Europe and Asia. H. sapiens replaced the local forms without hybridization. No genes from these earlier forms persist in modern human populations.
        2. (b) The hybridization and assimilation model. According to this model, modern H. sapiens evolved in Africa and then migrated to Europe and Asia. H. sapiens largely replaced the local populations, but there was hybridization between the newcomers and the established residents. As a result, some genes from the archaic local populations were assimilated and persist in modern human populations.
        3. (c) The multiregional evolution model. According to this model, H. sapiens evolved concurrently in Europe, Africa, and Asia, with sufficient gene flow among populations to maintain their continuity as a single species. Gene pools of all present-day human populations are derived from a mixture of distant and local archaic populations.
        4. (d) The candelabra model: H. sapiens evolved independently in Europe, Africa, and Asia, without gene flow among populations. All genes in present-day European and Asian populations are derived from local archaic populations.
    12. Figure 20.21 Phylogenetic predictions of the African replacement model versus the multiregional evolution model.  (a) The African replacement model predicts that all modern humans will be more closely related to each other than any is to any archaic species and that, among the archaic species, those from Africa will be the most closely related to modern humans. (b) In contrast, the multiregional evolution model predicts that the archaic and modern humans in each region will be each other's closest relatives. From Lieberman (1995).
    13. Figure 20.22 Phylogeny of Neandertals and modern humans.  This cartoon summarizes evidence from analyses of mitochondrial DNA sequences from several hundred modern humans and three Neandertals. The split between Neandertals versus humans predates the diversification within each lineage by a substantial margin. This suggests that modern humans are a distinct lineage from Neandertals and replaced them without hybridization. After Ingman et al. (2000), Krings et al. (2000), Ovchinnikov et al. (2000), and Hoffreiter et al. (2001).
    14. Table 20.1 Genetic distances between humans, chimpanzees, and gorillas
    15. Figure 20.8 Differences in gene expression patterns in different tissues of humans, chimps, and rhesus macaques
      1. These unrooted trees represent the divergence in overall patterns of gene expression in humans versus chimpanzees versus rhesus macaques. The numbers on the human branches represent the ratio of the human divergence versus the chimp divergence. In blood and liver, humans have diverged from the common pattern about as much as chimps have. In brain, however, humans have diverged considerably more.
    16. Figure 20.32 Brain size versus body size in a variety of hominins and great apes.  Data points represent species averages, with best-fit lines. In all three groups, species with larger brains have larger bodies. Australopithecines have larger brains for their size than extant great apes. Homo species have larger brains for their size, as well as a dramatically different relationship between brain size and body size. The extant great apes are the bonobo, common chimpanzee, orangutan, and gorilla; the australopithecines are A. afarensis, A. africanus, P. boisei, and P. robustus; the Homo species are H. habilis, H. ergaster/erectus, and H. sapiens. The data are from Tobias (1987) and Pilbeam and Gould (1974). See also McHenry (1994). After Pilbeam and Gould (1974).
    17. Human and ape ontogeny.

    Box 4.5  The Tree of Life -- or Perhaps the Web of Life

    1. Horizontal Gene Transfer
      1. Image from Wikipedia by Barth Smets: tree of life showing vertical and horizontal gene transfers.


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