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    Patterns and Process

    Humans see patterns in the world around them.

    When we observe patterns, we seek to find
    the processes that cause them.

    Many patterns in Nature can be explained
    by evolutionary processes.

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Evidence of Past and Ongoing Evolution

    Any theory of the evolution of life must explain
    these patterns.

      1. Life on earth is diverse (interspecific variation)

      2. All life on earth can be joined in a single phylogeny.

      3. There is genetic diversity within species.
      xxx (intraspecific variation)

      4. Organisms exhibit adaptative traits.

      5. Organisms also exhibit maladaptative traits.

      6. Biodiversity is not constant.

        • 6a. Biodiversity varies across time.
        • 6b. Biodiversity varies across geographic space.

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    Pattern 1: Diversity of Life

    EMPIRICAL FACT:
    There are 5 - 50 million species on our planet.
    Of these, only 1.5 million have been named and described.

    Living organisms are, essentially, variations on a theme.

    Why so many species?

      Why not just one?
      Why not 10?
      Why not a few thousand?

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    Pattern 2: The Tree of Life

    EMPIRICAL FACT:
    DNA sequencing reveals that
    • The genomes of humans and chimpanzees are 98% the same.
    • The genomes of Old World Monkeys and Great Apes are 93% the same.
    • The genomes of New World and Old World Monkeys/Great Apes are 89% the same.

    This pattern continues as one compares the DNA of other species.
    More branches can be added to show the relative similarity of all living things.

    The branching diagram representing these relationships is a phylogenetic tree

    • The tree makes no inferences about reasons for these similarities.
    • It is simply an empirical observation, a fact.

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    EMPIRICAL FACT:
    All life on earth fits on a single phylogenetic tree, the "Tree of Life".
    It is possible to devise this tree because

    • all species on earth use exactly the same heritable material, DNA
    • the DNA in each species varies incrementally
    • the more similar the species' phenotypes, the more similar their DNA

    The mechanisms of DNA replication, transcription, and translation
    are essentially the same in all species.

    EMPIRICAL FACT:
    DNA composition is arbitrary.

    • There is nothing special about the A,C,T,G nucleotides.
    • A vast number of other nucleotides would work just as well (perhaps better).
    • Codons (three-base combinations) are even more arbitrary.
    • Yet the genetic code is the same in all species.

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    EMPIRICAL FACT:
    All life can be reconstructed by a series of slight modifications of form.
    • Each species appears to be a slightly modified version of pre-existing species.
    • Closely related species are slight modifications of one another.
    • There is no functional or design reason for this.

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    EVOLUTIONARY INFERENCE:
    The Tree of Life looks like a family tree because it is one.

    All life on earth is related by descent from a common ancestor.

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    EVOLUTIONARY THEORY:
    All existing species arose by means of evolution, descent with modification.

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    Evidence for Modification: Homology

    How many cervical vertebrae are present
    in each of the species pictured at the left?

    Fun trivia: Do any mammals differ in their number of cervical vertebrae?

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Homology: Vertebrate forelimb bones

    Homology: Morphology

    Over evolutionary time, countless characteristics can change from ancestor to descendant.
    • vertebrate bones
    • plant organs (root, stem, and leaf)
    • protist organelles and ancillary structures
    • thousands more

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Homology: Vertebrate embryos

    Homology: Embryo Development

    Ontogeny (= ontogenesis, morphogenesis) is the origination
    and development of an organism.

    It is the developmental process occurring from fertilization --> mature form.

    Differences in ontogeny among species are not trivial.

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    Ontogenetic Homologies

    Differentiation of homologous structures can
    be seen in developing embryos.

    Developmental innovations can provide raw material
    for the evolution of entirely new lineages.

    In embryo development, Timing is Everything (<--required link!).

    More complex adult forms are the result of changes in embryo development.

    • changes in timing of trait development
    • reduction or loss of embryonic characters
    • greater complexity added as development proceeds
    • heterochrony (<--required link!)

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(click on pic for source)

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atavistic tail

    Atavism: When Silenced Genes Awaken

    Biological atavism is the reappearance
    of a lost ancestral trait.

    Embryos can develop characteristics in utero that disappear
    or fail to develop as they normally do in related species.

    • Whale embryo leg buds
    • Human embryo caudal (tail) vertebrae
    • Human embryo caecum and appendix

    Sometimes, silenced genes can mutate
    and regain partial function.

    Atavistic characters are small, non-functional
    reminders of our ancestry.

supernumerary nipples

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    Homology: Gene Sequences

    The more recently two species diverged from a common ancestor,
    the more similar their DNA sequences are.

    Hox Genes are a family of genes that
    control the identity of developing body segments.

    Hox Genes are extremely similar across species.
    Animals as different as insects and humans have homologous Hox genes.

    "How homologous are they?"

    Hox genes are sooooo homologous...
    A mouse Hox gene transplanted into a fruit fly will perform
    the same function in the fly as it does in the mouse.

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    EvoDevo

    Scientists in the field of Evolutionary Developmental Biology ("EvoDevo") compare developmental processes among different species in order to

    • infer the species' ancestral relationships

    • elucidate the evolutionary history of ontogeny

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    Homology: Synteny

    Synteny is the conservation of blocks DNA
    in compared sets of chromosomes.

    Two or more similar blocks of a genomic region
    can be deduced as derived from a the same ancestral genomic region.

    Syntenic DNA can be derived from

    • a common ancestral species
    • duplicated DNA from a single species (gene duplication, polyploidy)

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    Homology: Amino Acid Sequence

    Molecular homologies can be seen at the level of the protein product.

    The amino acid sequence of hemoglobin is more similar in
    closely related species than in more distantly related species.

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    Pattern 3: Adaptation

    FACT:
      Organisms are be exquisitely adapted to survive and reproduce
      in the environments in which they have evolved.

      EVOLUTIONARY INFERENCE: This adaptation is not random.
      The diversity of adaptations reflects the challenges met in each environment.

      EVOLUTIONARY THEORY: Natural selection is the process by which populations become better adapted
      to their particular enviroment from one generation to the next.

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    Pattern 4: Maladaptation

    FACT:
      Organisms are not perfectly designed.
      They have numerous design flaws and defects.

      Humans. We're a mess.

      • Our neck, knees, hips, and back are poorly designed for bipedalism.
      • Why? These structures evolved for hundreds of millions of years to optimize quadrupedal locomotion.

      • Our appendix does little except occasionally rupture.

      • Our postnatal dependency period is extremely long.
      • Why? Our evolutionary increase in brain/cranium size happened very quickly
        • Evolutionary increase in female birth canal size did not keep pace.
        • Instead, selection favored those who gave birth to more altricial young.
        • Even so, the rate of female and infant deaths during childbirth is astronomically higher than in any other mammal, even with modern medicine.

      But OH, that brain.
      Its very existence tells us it's worth the compromise.

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via GIPHY

    Evolutionary Compromise

      FACT:
        Certain traits may be well adapted to serve an individual
        in its particular habitat, but life requires multi-tasking.

        Organisms sometimes exhibit traits that can be described
        only as...imperfect.

      EVOLUTIONARY INFERENCE:

        Modification of existing structures forces design compromises.

        These would not be predicted if each species was built de novo (from scratch).

      EVOLUTIONARY THEORY:

        Phenotypic constraints result from evolutionary compromise.

        Examples:

      • A male guppy with brighter colors attracts more females,
        but the colors will also be more conspicuous to predators.
        Natural selection "compromises" on brightness.

      • Some body forms work better in water, some work better on land.
        Some species could live in either habitat, but make use of both.
        Their ultimate body plan is a compromise, naturally selected to work adequately in both.

      • A cheetah with longer legs could run faster.
        But longer legs mean more fragile bones.
        Natural selection results in an optimal length.

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What Process Can Explain These Patterns?

Recall the five patterns a valid theory must explain.