Presentation Notes II

by the members of CPSP118G Group II.

Erik Koentje

David Lund
Annette Murano

The History of Life
Evolutionary Processes I
Evolutionary Processes II
Phylogenetic Systematics
An Outline of Vertebrate Evolution

The History of Life

By Todd Metcalfe
Links identified by Robert Caslow
November 22, 1999

  1. Precambrian: time in the Earth's history that lacks obvious fossils

    A. Earth's crust started to form about 4 billion years ago.

    B. Oldest known crust dates from shortly after this time period.

    C. The first evidence of life is 4 billion years old.

  2. Processes of the early Precambrian were much like the modern Earth, with some notable exceptions:

    A. There was more geo-thermal power being released then.

    B. Continental plates only 40-100 km across, as opposed to thousands of km observed now.

    C. The Origin of Life

      1. In 1980's predominate thought focuses around calm pools of water as the place of origin.

      2. Now predominate thought focuses around geochemical processes occurring at seafloor vents in geologically active places like mid-ocean ridges.

  3. Evidence of life

    A. Around 4 billion years ago first direct evidence of life

    B. First forms of life were similar to the blue-green algae that built mounds called stromatolites

    C. Some time after the origin of life, some life-forms attained the ability to capture energy from sunlight using photosynthesis. This process produced oxygen as a byproduct

      1. This oxygen killed other life forms in the first great extinction event.

      2. Evidence is found in banded iron, found in the middle and later part of Precambrian period, which only forms under certain conditions of oxygen concentrations

  4. Late Precambrian

    A. There were two super continents, about the same size as today's landmasses.

    B. Possible that there was ice from pole to pole.

  5. Early Cambrian

    A. Phanerozoic: "age of visible animals;" from Cambrian to present.

    B. Familiar animals included:

      1. Trilobites, a kind of early arthropod

      2. Corals

      3. Crinoids

      4. Snails

    C. Early Vertebrates

      1. Started to emerge in this time period

      2. Sacabambaspis: 7 inches fish-like creature with a plated exoskeleton.

  6. Late Devonian: about 363 Ma

    A. Start of Appalachian Mountain chain

    B. Diversification of life

      1. Although all fish breathe primarily with gills, many early fish probably had lungs. The swim bladder, an organ used by many highly derived fish to maintain neutral buoyancy, is probably a modified lung.

      2. Early amphibians

        a. Had lungs and internal gills

        b. Mostly aquatic

      3. Plants started to colonize land in the Silurian period. By the late Devonian, the first forests of tree-sized plants were appearing.

    C. Land

      1. Plants and arthropods were first multicellular organisms onto the land.

        a. Many land arthropods were very large compared to their modern relatives. One possible explanation is that there was a higher concentration of oxygen in the atmosphere.

        b. It is also possible that large arthropods disappeared due to increased competition between them and land vertebrates.

      2. Next came reptiles

        a. Developed the amniotic egg, with leathery shell. This allowed them to reproduce on land, making them less dependent on water.

        b. Allowed vertebrates to fill more niches on land

      D. Vertebrate diversity takes off

  7. End of Paleozoic: 251 Ma

    A. Single largest die off of plants and animals in last half billion years

    B. Extinction occurred at the time of the single largest known series of volcanic eruptions. Whether one event caused the other is unknown.

    C. Among the animals that survived the extinction:

      1. Proto-mammals

      2. True reptiles

  8. Late Triassic: 225 Ma

    A. At this time, most of the world's land masses were assembled in the supercontinent "Pangea." Pangea, at this time, had a hotter and dryer climate, giving reptiles an advantage. Among the reptiles flourishing in this environment were:

      1. Archosaurs, the group that includes modern crocodylians and birds

      2. Close relatives of crocodylians inhabit the super continent

      3. Some reptiles move back into the sea, giving rise to marine reptiles such as ichthyosaurs and plesiosaurs.

    B. On land, some archosaurs evolve a posture in which their legs are tucked under their bodies.

    C. During the Mesozoic era dinosaurs become the dominant land vertebrates. Some examples include:

      1. Stegosaurs- This animal used and array of tail spikes, the "thagomizer" for defense from predators.

      2. Sauropods - the classic "Sinclair dinosaurs," gigantic herbivores with long necks and tails.

      3. Theropods - bipedal predators that included familiar varieties such as Tyrannosaurus rex and Allosaurus.

      4. A growing number of advanced theropods are known to have had an interesting specialization: feathers. One such creature, Archaeopteryx, has long been recognized as a close relative of living birds. Although it had feathers and could probably fly, it retained a long tail, clawed hands, and teeth. For all their differences, it appears that modern birds are also theropod dinosaurs

  9. Late Cretaceous: 70 Ma

    A. By this time, flowering plants, angiosperms, appeared and diversified

    B. Mammals- were diverse but inconspicuous. None was larger than a house cat.

    C. The Cretaceous gets its name from the Latin word "creta," which means "chalk."

      1. Several European chalk deposits (later to become cliffs) formed from this period

      2. In the seas, there were giant scallops and reef-forming oysters.

    D. Mass extinction wiped out many marine invertebrates and reptiles, and all non-avian dinosaurs.

      1. Evidence of a meteor impact near the town of Chicxulub in southern Mexico. Crater is estimated to have been 180 - 200 km across

      2. Large volcanic episode around the same time covered much of India with flood basalts

      3. Scientists speculate that these events helped to drive extinctions

  10. Cenozoic

    A. Mammals dominate life form on land. Mammalian diversity explodes. Among the mammalian groups are primates, including lemurs, monkeys, apes, and humans.

    B. During late Cenozoic, environmental changes in Africa force some primates to abandon the trees for open country. One such group gave rise to humans within the last ten million years.

Evolutionary Processes Part I: Early Evolutionary Thought and the Career of Charles Darwin

By: Fern Gookin
December 3, 1999

In the 17th and 18th centuries, before the theories of Charles Darwin were accepted, many people had their own ideas about the species on the planet. One popular theory was that of Bishop Usher. Based on dates in the bible, this Irish cleric estimated the earth's creation was precisely on October 26, 4004 B.C. Also prevalent at the time was the idea of plenum, which stated that God populated the Earth and would never add or deplete any organism. Therefore, this left no room for creation or extinction. Then, in 1770 the remains of a Mosasaurus were found. Now Bishop Usher's ideas were put under severe pressure.

After this discovery, more theories began to develop. Georges Curvier, the father of vertebrate comparative anatomy, suggested that this Mosasaurus may be the remains of a giant lizard which had gone extinct. This concept of extinction was now looked at more closely. For example, scientists examined the case of the great auk; an animal believed to have gone into extinction. Now, the new proposal was: if species can be extinct, they must be able to come into being as well. This idea contradicted Bishop Usher; everything could not have happened at one time.  The early evolutionist, Jean-Baptiste Lamarck now began his experiments.  Lamarck recognized that the diversity of living things could be the result of descent with modification, or evolution.  He made many attempts to prove this and failed.  Evolution was now a revolution waiting to happen.

Always at the center point of the history of evolution is Charles Darwin.  In 1839, he got a job as a captain's companion on the British research vessel the HMS Beagle, under captain Fitzroy.  Little did Darwin know that on this trip he would change the theories about evolution forever.  On this voyage, Darwin visited the Galapagos Islands and recognized that each island had its own unique but similar species.  He was amazed to see not only the variations within the islands, but also the difference in the species there from those in England.  Darwin kept a journal on his evolutionary discoveries but kept them quiet.  Nearly twenty years later in 1858, Alfred Russell Wallace wrote a letter to Charles Darwin containing many of the same ideas and discoveries Darwin had made on his voyage.  These men began to share ideas, and Charles Darwin immediately wrote a book about their findings.

In 1859, the first edition of Darwin's Origin of Species sold out on the first day.  In this book, Darwin discussed the idea that there is both individual variation and natural selection (preservation of a favorable variation) occurring within the populations of the world. Each individual, therefore, is equally legitimate.  Darwin suggested that there must be some natural force that plays the role of the human breeder.  Darwin also set up a principle of an all encompassing rule -- the theory of evolution. This acknowledged the important connection between reproduction and the extinction and creation of species.

By his death in 1882, Darwin had already critically changed and gotten support from the academic community.  But even Darwin couldn't figure out exactly how it all worked.  In 1865, Gregor Mendel made important discoveries about genetics. However, it wasn't until the 1900's that Mendel was rediscovered and the fundamentals of evolution and genetics were synthesized.  New ideas began to emerge from this connection.  For example, pleiotropy was introduced.  This idea concluded that genes ride along to the next dominant gene, changing the characteristics of the organism.  Then, there was the concept of genetic drift -- evolution results from random events and functions most powerfully in small populations.  Another major concept was the idea of sexual selection -- animals only mate with a member with certain characteristics; therefore the population is bound to evolve favoring those attributes.

Together, these theories revolutionized the scientific community.  There is no dispute among biologists about these mechanisms, but there are many disputes about the fine-tuned details.  Many people are still confused about the concept of evolution and base their rejections on false statements.  Most commonly, people attack evolution because they think it is attempting to explain the origin of life.  This is not true.  Evolution is descent with modification, it makes no attempt to postulate how species were first created, only their changes over time.  It is also thought that evolutionists try to explain the origin of humans.  Once again, this is a false interpretation.  Scientists do not know exactly how humans came into being.  Evolution is also twisted as a prescription for human society.  This is completely erroneous, since evolution is a natural process and not to be modified by human efforts.  

Processes of Evolution

By Edward Peckham
December 3, 1999

  1. Definition: The diversity of life is the product of descent with modification, one of the most important unifying themes in biology. What this means is that when organisms reproduce, their offspring possess traits that are similar to their parents'. Sometimes these traits, for various reasons, are modified. When offspring with this modified trait mate, the trait is passed on to the next generation causing it to spread further through the population. This subtle change over time is responsible for the huge biodiversity that we have on this planet.

  2. Evolutionary Processes: These describe the natural mechanisms that drive evolution.

    1. Natural Selection: Within every generation, there is a certain degree of variation. Each individual in a population is slightly different than all the others. These differences are caused by the random combination of genes from the parents and an equally random chance of mutation within each gene. Sometimes, a new mutation endows the individual with a trait that gives it an advantage over the other individuals in its community. This advantage causes it to have a better chance at mating and producing offspring. Since the genes of this individual's offspring also contain this desirable trait, then it's offspring will be more likely to mate and produce more offspring, thus the new trait becomes more and more prolific in the community. On the other hand, a trait that is disadvantageous will cause the individual possessing it to be less likely to reproduce. This negative trait will then occur less and less in future generations until it is completely absent. Consider the photo of the frog with eyes in its mouth. This mutation caused a trait that made it difficult for the frog to see. It most likely was unable to mate successfully with many females since it couldn't see them. Because the frog was unable to mate, the gene containing the mutation could not be passed on to the next generation, therefore removing a detrimental trait from the population.

    2. Sexual Selection: Ask yourself this question: "Would I mate indiscriminately with anyone on campus of the opposite sex?" Most people would answer "no" to this question, and so would most other organisms. In every species possessing two sexes, there is the issue of mate selection. Unlike mutations and meiosis (the dividing up of chromosomes between sex cells), organisms do not pick their mates at random. Their chances of mating depend on certain traits that are considered desirable by the opposite sex. The more noticeable the trait, the better chances a mate will be attracted to it. Since the primary goal of all living things is to pass on its genetic information to a new generation, many complicated, and in other ways not necessarily advantageous traits have evolved to ensure the attraction of potential mates. An example would be the peacock. The male peacock has an extremely large and extravagant tail that it fans out to attract females. While having a large tail gives the male a better chance to mate, it also gives it a better chance to be caught by a predator. Also consider how a population would be affected if all the members of one sex decided to only mate with individuals possessing a certain trait. For example, what if all females on in the world decided to only mate with males who had red hair? After a few generations, the representation of red hair would much exceed that of any other hair color. This illustrates another way in which sexual selection can affect evolution.

    3. Heterochrony: Every creature has some sort of developmental path that leads it from a single cell form to a mature organism. This developmental path is called a creature's ontogeny. Heterochrony describes an evolutionary change in an organism's ontogeny. The results of this could affect the rate at which organisms develop. In some cases a new species will arise that reaches maturity at a level that would be considered juvenile in the parent species. Humans are an example of this. We possess very large heads in proportion to our bodies in adulthood. That trait in chimps, our closest biological relative, is attributed to infants.

    4. Pleiotropy: Pleiotropy describes gene hitchhikers. This occurs when a trait that is neither advantageous nor disadvantageous is perpetuated by another, advantageous trait. This happens when the gene for the neutral trait is located very near the gene for the advantageous trait on a chromosome. Whenever a mate selects an individual with a neutral trait because it also has an advantageous trait, the neutral trait is inadvertently being passed to the next generation as well.

    5. Drift: Genetic drift is the random dispersion of traits throughout a population. In a large population, drift usually does not affect the successive generations to a large degree, but as a population gets smaller, the influence of each individual on genetic drift increases. Consider a population made up of 100 individuals randomly selected out of the student body. If you look at the resulting population a few generations later, you will most likely find that any one member of the original population does not heavily influence each individual's traits. Now what if the original population consisted of only 4 individuals? The individuals in the resulting generations would look very much like the individuals in the original generation. So, within small populations, genetic drift has a very powerful affect on evolution.

Phylogenetic Systematics

By Sung Kim
Images obtained by James Porter
December 2, 99

The phylogenetic system was created in order to organize the vast diversity of living things according to natural evolutionary history or phylogeny. The tree of evolutionary history can be pcitured using diagrams called cladograms. Cladograms are, in a sense, a family tree. Rather than "family" members occupying each branch of the tree, cladogram branches contain organisms that are related by patterns of evolution. As a result, cladograms have a much broader and exotic tree compared to most of our own family trees.

A cladogram is organized according to the path of changes in a group of organisms. Older, ancestral lineages are shown branching and giving rise to newer descendant lineages. The oldest in the evolutionary chain are shown at the bottom and the youngest are at the very top, like branches of a real tree. As a result, it's logical that the tree's time reference approaches present day as it rises.


A taxonomic systems is a classification of organisms. There are many different kinds. The phylogenetic system uses phylogeny as its organizing principle. Because it is based on phylogeny, which can be visually represented by the cladogram, the cladogram is often used both to show evolutionary history and to show the taxonomic groups of the phylogenetic system. This organization allows scientists to visualize the branching history of evolving lineages - the tree of life.


Everything in the phylogenetic system is organized and defined based on descent from a common ancestor. Some terms used to associate the groups of organisms are monophyletic, paraphyletic, and polyphyletic groups. Monophyletic groups are an ancestor (that is, an ancestral interbreeding population) and all of its descendants. Paraphyletic groups are ancestors and some but not all of their descendants. Finally, polyphyletic groups are organisms which fail to include some of their common ancestors. Note that even though we talk about paraphyletic and polyphyletic groups, monophyletic groups are the only kind of group recognized as valid in the phylogenetic system. This is because they are based on non-arbitrary criteria: descent from a real common ancestor.

How do we know about evolutionary history? In order to reconstruct a section of the tree of evolution and show it as a proper cladogram, we need information about organisms and their traits. Such information can be assembled in a matrix, a simple table containing the names of the organisms and a set of traits. By examining this table, we can make a hypothesis of the evolutionary history of these traits, and use them to arrange the branches on the evolutionary tree.


Our goal is to organize organisms into internested groups, each one of which is descended from a single common ancestor. The key to achieving this is to identify "synapomorphies." Synapomorphies are shared derived traits. Organisms that have evolved from the ancestor in which a new, or "derived" trait appeared will inherit this trait. Synapomorphies, therefore, act like marker dye injected into the growing evolutionary tree, enabling systematists to identify the organisms that share relatively recent common ancestry. When potential synapomorphies are identified, they are mapped onto the various alternative arrangements of the evolutionary tree. The version that accounts for the distribution of derived traits while requiring the fewest possible character state changes is called "the most parsimonious." It is our best hypothesis of evolutionary history.

Phylogenetic systematics can be very useful, as it provides a means to organize life on earth, as well as being a tool to tell us the history of life. Therefore it is very important to always make sure the information and criteria we use to create cladograms is reasonable. Otherwise, the whole pattern of evolution and life on earth will be incorrect from the point after the mistake. Just imagine: because of one mistake we could be identified as the descendants of apple trees.


A Walking Tour of Vertebrate Evolution

by Tak Kei Lee
Images obtained by Andrew Taylor
November 30, 1999


The evolution of the vertebrates began with the development of a head containing a brain and special sense organs at the front end of the central nervous system. These structures were encased in a bony cover, the skull. Before this happened, many important evolutionary developments had taken place among the closest invertebrate relatives of the vertebrates. These included the development of a central nervous system consisting of a spinal cord which was protected by a primitive spine. An example of this is Amphioxus, a fish-like organism with a mouth and spine but without a distinct head.

As these organism evolved, they developed jaws and other derived features, becoming proper fish. The evolution of fins allowed greater control of swimming. Slowly with more active organisms fighting for the resources in the sea, some fish evolved the ability briefly to search for food on land. This led to the appearance of land vertebrates.


However, land animals did not just appear, for the ancestors of land vertebrates were not equipped to move about, breathe, or use their senses on land. In the first of these land vertebrates, fins were modified into feet and legs. The lungs, auxiliary breathing structures in bony fish, replaced gills as the primary breathing apparatus. These are not their only evolutionary novelties. On their limbs were individual digits. Their eyes evolved to cope with the refraction of light as it entered their eyes from the air. Desiccation-resistant skin also evolved, allowing them to spend time away from water. These advances may have been spurred by the fact that during the late Devonian, when land vertebrates first appear, there were abundant food source and virtually no predators on land, while in the sea food was scarce and predators were not. These creatures gave rise to all later land vertebrates. In their way of life, they resembled some of their modern descendants, the amphibians.

For all their advancements, these organisms still depended on bodies of water for on thing, reproduction. Their reproductive cycles required them to lay egg in the water. This dependency was broken by the evolution of the amniotic egg, whose water-tight membranes encloses a tiny "pond" in which the embryo could grow. These eggs made the organism that possessed it, the amniotes, less dependent on water. From the common ancestor of amniotes evolved such diverse creatures as dinosaurs and humans.

As these organisms evolved, they gave rise to several major lineages, including:

Each group has its own distinct attributes. For example, the archosaurs practice nest building and parental care of young. Therian mammals are warm-blooded and give birth to live young.