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The Fact of Evolution: Observable Evidence

Despite what some might believe, the physical evidence that evolution has happened via natural processes is overwhelming.
While some may wish to invoke the intervention of a higher power, this is not necessary to explain evolution.

This might not have been the case in Darwin's time.
But since the publication of On the Origin of Species, a great deal more has come to light.

There are at least four major lines of physical evidence telling us that evolution has occurred, and is still occurring.

Species and Speciation
Recall the biological definition of a species.

Speciation is the generation of two (or possibly more) reproductively isolated new species from an ancestral species.

Speciation implies that the two new species are no longer able to produce fertile, viable offspring with each other: they are reproductively isolated.

Lines of Evidence: What Rocks and Fossils Tell Us

Despite what you might have heard, fossils are NOT the best line of evidence for evolution.
However, they offer a "snapshot" into various eras of the past and the organisms that lived in those times.
Fossils show us how life has changed over time, with species appearing, giving rise to new species, and often going extinct.

Paleontology and Geology were the first scientific disciplines to yield information indicating that earth was more than a few thousand years old.
Countless mountain ranges filled with marine fossils tell us that the earth we see today was very different long ago.

The oldest layers of sedimentary rock comprising the mountains around Convict Lake in the Sierra Nevada
(more than 200 miles inland from San Francisco, CA) contain 400-million year old marine fossils.

Note that fossils are rare. Most organisms are consumed and destroyed relatively soon after they die. Only rarely do properties of the organism and environment promote fossilization. If you're going to become a fossil, it helps to have...

What are Fossils?
Fossils can be organismal body parts, or they can be trace fossils, evidence left by living organisms.

Fossil bodies or body parts can be unaltered (composed of actual matter from the organism):

...or they can be altered Trace fossils include things like These can be used to track changes in biodiversity and body forms over evolutionary time.

Determining the Age of Fossils: Relative vs. Absolute Dating

Before radiometric dating techniques were invented, paleontologists were able to compare the age of fossils and rocks with relative dating.

Relative Dating
Stratigraphy is the study of layers (strata) of sedimentary and volcanic (=igneous) layered rock.

Some common forms of sedimentary rock include

How does sedimentary rock form?
Erosion by wind and water over millions of years gradually wears away particles of earth and washes them into bodies of water (streams, rivers, oceans).
As these particles settle to the bottom, they solidify.
As more layers are laid on top of older ones, the lower layers are compressed, and eventually turn into rock.

Geologists represent such formations as a stratigraphic column, which describes the vertical placement of rock layers/units in a particular location.

Geological Principles

  • Principle of Superposition - Older layers of sediment are covered by younger/newer layers. The most recent layers are at the top.

  • Principle of Fossil Succession - If organisms evolve and change over time, then specific species found in a particular layer can be used as age markers, linking geographically distant sediments to the same time frame. Any pebbles, fossils, or other fragments embedded in sedimentary rock must be older than the rock matrix itself.

  • Principle of Cross-cutting Relationships - Intrusions that cut through sediments must be younger than the sedimentary layers they cross.

  • Principle of Deformation - Sedimentary rocks that have been deformed by folding, lifting or other malformation must be older than the event that changed them.

    Using these principles, geologists can determine the relative age of fossils embedded in sedimentary rock.

    Absolute (Radiometric) Dating
    To determine the absolute age of a fossil, radiometric dating techniques must be employed.

    Molecules usually exist in a stable form that does not release any of its subatomic particles.
    However, sometimes a molecule may exist as an isotope.
    Isotopes are atoms of the same chemical element that differ only in their number of neutrons.

    A radioactive isotope is one with an unstable nucleus. To become stable, the atom emits ionizing radiation (alpha and beta particles or gamma rays). In the process, the nature of the particles in the nucleus changes, and the radioactive substance becomes a stable isotope of a different element.

    Example: Carbon


    The half life of a specific isotope is the time needed for half the nuclei in a sample of it to decay to its stable form. After one half life, one half of the original sample will remain radioactive. After two half-lives, one fourth of the original sample will still be radioactive; after three half-lives, one eighth of the original sample will still be radioactive, etc.

    Specific isotopes have known rates of decay and known half lives. For example:

    The relative proportions of a radioactive isotope and its decay products in a sample tells us how much time has elapsed since the sample was formed.

    The greater the proportion of decay product to radioactive isotope, the older the sample.

    Different elements and isotopes must be used to date different types of fossils.

    For example, carbon-dating is used to determine the age of relatively recent fossils such as the Bog People.
    Uranium or rubidium decay rates are used to gauge the age of very ancient things, such as the earth itself.
    ~ ~ ~ ~ ~
    Unlike relative dating, absolute dating of fossils involves establishing a discrete age (in years) of the fossils under study.

    Lines of Evidence: Homologies

    First, let's establish how evolution does NOT happen.

    A question sometimes posed by people who do not understand evolutionary mechanisms is:

    "If humans evolved from monkeys, then why are there still monkeys?"

    Very simply:

    How do we know?

    If you go back far enough, all species are derived from a common ancestor.

    That means...

    ...but they do all share a common ancestor, if you go back far enough.

    One of the most powerful forms of evidence for the common descent of all living things is homology.

    In biology, a homology is a characteristic shared by two species (or other taxa) that is similar because of common ancestry.

    1. Morphological Homology

    Structures derived from a common ancestral structure (that may or may not be used for the same function in the species in which it occurs) are called homologous structures.

    A classic example of homology is seen in the skeletal components of vertebrates...

    Evolution can be considered a process of "remodeling" a population over the course of many generations, with one of the main the driving forces being the natural selection factors that favor one form over another in specific environments.

    Scientists have several criteria for determining whether structures are homologous.

    Let's have a look at some of our own homologies in The Zoo that is YOU.

    Shared homologies allow us to devise hypothetical "family trees" of living organisms called phylogenies.
    These can be represented as a branching diagram called a phylogenetic tree or evolutionary tree.

    The three purple hashmarks on the tree represent evolutionary innovations shared by all the groups above it (i.e., to the right) on the tree. Such shared characters allow evolutionary biologists to determine common ancestry.

    Homology: Clue to Shared Ancestry

    Just as physical similarities among siblings provide evidence that they are related to each other,
    physical similarities between species tell us that they are related.

    Just as humans change across generations, so, too, do natural populations of other species.
    By comparing the traits of species that are both closely and distantly related to each other, we can begin to understand their evolutionary history.

    Primitive and Derived Characters

    We can learn about the process of evolution from studies of both extant and extinct species, and comparing their physical and chemical characteristics.

  • A primitive character (plesiomorphy) is one that is relatively unchanged from its original, ancestral form.
    Example: Like the very first ancestral vertebrate, all modern vertebrates have a bony tail posterior to the anus.

  • A derived character (apomorphy) is one that is relatively modified from its original, ancestral form.
    Example: Many vertebrates have highly modified versions of the post-anal tail.
    The reduction of the tail in great apes (including humans) is an example.

    The long tail of the baboon is a more primitive condition than very reduced (derived) tail of the gorilla or the Very Handsome Man

    Latent Genes Can Awaken

    Occasionally, we get an atavistic reminder of our ancestry.

    The Atavistic Human Tail
    (still don't believe we're related to monkeys?)

    And then there are those pesky supernumerary nipples.

    Some humans have fully developed nipples running along the ancestral mammary line.

    Symplesiomorphies and Synapomorphies

    Note that "primitive" and "derived" are relative terms.
    You can't call something "primitive" or "derived" without comparing it to something else.

    When you invoke the "primitive" or "derived" state of a particular character,
    you are examining homology between two or more species derived from a common ancestor.

    Systematists often use the existence of homologous, shared characters among taxa to help reveal their common ancestry.

  • The more recently two species diverged from a common ancestor, the more synapomorphies they will share.

  • Unique synapomorphies found only in a particular group of organisms provide strong evidence for the common ancestry of members of that group.

    Homology Reveals Relatedness

    The synapomorphic astragalus ankle bones of ancient whales (Cetaceans) and cloven-hooved mammals (Artiodactyls) helped biologists determine that these two groups share a relatively recent common ancestor.

    When you're trying to determine common ancestry, synapomorphies are far more informative than symplesiomorphies.

    To illustrate this, let's consider our own species and some of our closest vertebrate relatives.

    (See what you missed if you didn't come to class?)

    Analogous Structures: Convergent Evolution

    Structures can appear similar for reasons other than common ancestry.

    An analogous structure found in two different species

    Example: The wing of a butterfly and the wing of a bat.

    How do we know the common ancestor of the butterfly and the bat didn't pass on the wings to both species?

    To fully understand how we know the wings evolved independently, we must take a trip deep into the past, to meet the last common ancestor of the bat and the bird.

    During ontogeny (embryo development), all animals go through this progression:

    The last stage shown in the diagram is known as a gastrula.
    It's the first point in animal development where there is a MOUTH.
    At the gastrula stage, the mouth is known as the blastopore.

    During the ontogeny of a butterfly and a bat, the gastrula stage is pretty much where developmental physical similarity between them ends.

    After gastrulation

    Protostomes vs. Deuterostomes

    More than 520 million years ago, a genetic change in one lineage of animals caused the blastopore to develop into an anus instead of a mouth.
    From this ancestral change, the animal lineage we know today as the DEUTEROSTOMES arose.

  • Animals whose blastopore becomes the mouth (the primitive condition) are known as protostomes
    (from the Greek proto, meaning "first" and stoma, meaning "mouth")

  • Animals whose blastopore becomes the anus (the derived condition) are known as deuterostomes
    (from the Greek deutero, meaning "second" and stoma, meaning "mouth")


    In most animals, the blastopore becomes the mouth:

    • jellyfish, corals, sea anemones (Cnidaria)
    • comb jellies (Ctenophora)

    The bilaterally symmetrical among them are protostomes:

    • flatworms (e.g., Platyhelminthes)
    • roundworms (Nematoda)
    • segmented worms (Annelida)
    • mollusks (Molluska)
    • water bears (Tardigrada)
    • arachnids, insects, crustaceans (Arthropoda)


    But in one lineage, a genetic change caused the blastopore to develop into the anus. This lineage comprises the deuterostomes:

    • starfish, sea urchins, etc. (Echinodermata)
    • acorn worms (Hemichordata)
    • tunicates (Urochordata)
    • lancelets (Cephalochordata)
    • vertebrates (Vertebrata)

    Back to Butterfly and Bat Wings...

  • Butterflies (Arthropoda) are protostomes.
  • Bats (Vertebrata) are deuterostomes.
  • The most recent common ancestor of a butterfly and a bat existed hundreds of millions of years ago
  • It may have looked a bit like today's gastrula (A hypothetical creature called a gastrea, sexually mature gastrula--no wings.)

    Or possibly the slightly fancier Urbilateria, a simple flatworm that was barely more than a crawling gastrula, at least in some depictions.

    The ancient last common ancestor of the butterfly and the bat had nothing like wings.
    This tells us that the wings of the butterfly and the wings of the bat evolved independently, long after their ancestral lineages diverged from the gastrula-like ancestor.

    The same developmental toolkit may be used to generate analogous structures in distantly related animals.

    Happy Accidents

    Stephen Jay Gould first coined the term exaptation: a functional character initially with no known adaptive significance (i.e., not a product of natural selection).
    In a changing environmental context (and hence, changing selection pressures) an exaptation may confer a selective advantage that it did not initially confer.

    Flight (certainly an adaptive function) may have been a "happy accident"--an eventual outcome these original functions.

    But beware the danger of slipping into the "Just So Story".

    Vestigial Characters: Highly Derived and Mostly Non-functional

    A vestigial structure is one that has marginal, if any use to the organism in which it occurs.
    These are some of the most interesting examples of homology. Why do structures become vestigial? Is it, as Lamarck suggested, a case of "use vs. disuse"?
    Modern hypothesis: It's all about natural selection.
    Let's discuss...

    2. Ontogenetic Homology

    The study of embryo development is one of the hottest areas in evolutionary biology, the study of the evolution of development (a.k.a., evo-devo).

    Ever heard the phrase, "Ontogeny Recapitulates Phylogeny"?

  • ontogeny is the process of embryo development (from the Greek onto, meaning "being" or "existence" and genesis meaning "origin")
  • phylogeny is a species' evolutionary history (from the Greek phyla, meaning "tribe" and genesis meaning "origin")

    The phrase above was coined by German physician Ernst von Haeckel, who quit his medical practice to become an apologist for evolution after reading Darwin's On the Origin of Species by Means of Natural Selection.

    Haeckel was the first to notice that the embryonic forms of different species had remarkable physical similarities.
    He suggested that every living thing passes through its evolutionary history during its embryo development.

    While he didn't quite get his wording right (embryos don't actually pass through the adult forms of all the species that came before them), it is true that ontogenetic similarities across species reflect those species' common ancestry.

    Differences in ontogeny among taxa are not trivial.

    Such changes reflect the evolutionary relationships of those taxa, and the modified development that resulted in one species becoming two.
    Developmental innovations may have provided the evolutionary "raw material" for the origin of entirely new lineages.

    The claws of the baby hoatzin also fall into this category.

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

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

    Changes in the timing of ontogenetic events (between related species) is known as heterochrony(<--required link!).

    Consider members of the Phylum Chordata.
    At some point in their development, all members of Chordata show these traits, which are unique to Chordates:

    In early chordates (Cephalochordata - the lancelets), the notochord persists throughout the life of the organism:

    In somewhat more derived chordates (Urochordata), the notochord is seen in the larval form, but lost in the adult:

    And in the most derived chordates (Vertebrata), the complete notochord is seen only in early embryos, and becomes the discs between the vertebrae in the adult.

  • Heritable ontogenetic changes ultimately are reflected in the adult.
  • The ontogeny of the notochord in the three subphyla confirms common ancestry.

    3. Molecular Homology

    The molecules that carry the instructions for constructing and running the living organism--DNA and RNA--show homology across species.

    The more recently two species descended from a common ancestor, the more similar their DNA sequences.
    DNA encodes instructions for every living thing on earth. This in itself is powerful evidence of common ancestry.

    Hox Genes: Duplications and Conscription

    Whether it's a fruit fly or a mouse, homeo domain (Hox) genes are expressed every animal species known, and in a specific order that corresponds to the anterior --> posterior body axis.

    Homeodomain regions of Hox proteins show little variation across species, though 500 million years have passed since they last shared a common ancestor.

    (The homeodomain is NOT amenable to mutation.)

    Addition of complexity over time may be partly due to duplications of Hox complexes.

    In mice and other vertebrates, there are four Hox complexes on four different chromsomes, and each complex includes 9-11 genes, for a total of 39 Hox genes in vertebrates.

    Hox gene mutations cause changes the identity of the segment affected by the gene's action. The Hox genes are homologous among all animal species.

    Chromosomal Homology: Synteny

    We can see common ancestry in the chromosomes:

    Protein Homology

    Molecular homologies also can be seen at the level of the finished protein product encoded by the DNA, as shown in this comparison of amino acid sequence in hemoglobin (the protein in your red blood cells that carries oxygen) of different species:

    Most modern evolutionary biology is the study of molecular homology.