Chapter 20 The Macroevolutionary Puzzle
I. On Floods and Fossils
A. Traditional explanations of rock formations and fossils relied on effects of the Deluge.
B. Modern geologists view the same evidence as showing changes in geology and living organisms through time.

II. Evidence of Macroevolution
A. Macroevolution refers to the large-scale patterns, trends, and rates of change among higher-taxa groupings of species.
1. Evolution proceeds by modifications of organisms that already exist.
2. “New” species emerge as mutation, natural selection, and genetic drift change allele frequencies in reproductively isolated populations.
B. The Fossil Record
1. A fossil is recognizable, physical evidence of an organism that lived long ago—skeletons, shells, leaves, seeds, tracks.
a. For fossil formation, body parts or impressions must be buried in rock before decomposition.
b. Fossil records vary according to type of organism (hard parts preserve well, soft parts do not), stability of the geographical region (sea floor vs. eroding hill), and quality of the specimen.
2. The fossil record is far from complete, but some lineages are extensive.
C. Dating Fossils
1. Deepest rock strata are assumed to be the oldest, surface layers the youngest.
2. Fossils in these layers were the basis for dividing earth history into four eras: Proterozoic, Paleozoic, Mesozoic, Cenozoic (further research has added Archean before Proterozoic).
3. Radioactive dating methods have been used to assign dates to these eras.
D.Comparative Morphology
1. Evolutionary history is reconstructed on the basis of observed patterns of body forms.
2. Stages of Development
a. Different organisms may show similarities in morphology during their embryonic stages that often indicate evolutionary relationships.
b. Such similarities are one of the reasons why fishes, amphibians, reptiles, birds, and mammals are said to belong to the same phylum.
c. Some of the variation seen in adult vertebrates is due to mutations in regulatory genes that control the rates of growth of different body parts.
3. Homologous Structures
a. These are body features that resemble one another in form or patterning due to descent through common ancestors.
b. In morphological divergence, features have departed in appearance and/or function from the ancestral form (example: bones in forelimbs of vertebrates).
4. Analogous Structures
a. Analogous body parts are used for similar functions in dissimilar and distantly related species.
b. Morphological convergence is the adoption of similar function over periods of time but with no purposeful direction (example: fins in sharks, penguins, and porpoises).
E. Comparative Biochemistry
1. Neutral mutations have no more measurable effect on survival and reproduction rates than do other alleles for the trait; they accumulate in the DNA and can be used as a “molecular clock” for dating times of divergence of species.
2. DNA Comparisons
a. The degree of similarity of nucleotide sequences of DNA reveals information about evolutionary relationships.
b. If a single strand of DNA from one species is allowed to recombine with a single strand of DNA from another species, the degree to which they match up is a measure of similarity.
3. Protein Comparisons
a. Because genes dictate the sequence of amino acids in proteins, analysis of proteins can determine the similarity of genes between species.
b. For example: The amino acid sequence of cytochrome c shows strong evidence for placing humans, chimps, and rhesus monkeys in the same group.

III. Taxonomy
A. Recognizing Species
1. Units of evolution are called taxa, and the unit most often studied is the species.
2. Lineages are groups of populations that maintain genetic contact but have followed different evolutionary pathways.
a. Sometimes members of the same species do not look alike because of age or sex differences.
b. Alternatively, some organisms may appear nearly identical but be of different evolutionary lines.
3. Correct identification of species requires knowledge of anatomy, biochemistry, physiology, ecology, and behavior.
B. The Linnean Scheme
1. The binominal system was originated by Carl von Linné, better known as Linnaeus.
a. The first part of the scientific name was the genus (always capitalized and italicized) and signified very closely related organisms.
b. The second part was the species (never capitalized but always italicized) and signified an even closer, interbreeding relationship.
2. Other levels in the hierarchy were family >> order >> and kingdom.
3. The language used for scientific names is Latin for universal recognizability.

IV. Phylogeny
A. Three Interpretive Approaches
1. In “evolutionary systematics,” fossils are used in an attempt to reconstruct the past and provide clues to present relationships.
2. In “phenetics,” the reliance on similarities alone is the basis for groupings.
3. In “cladistics,” or “phylogenetic systematics,” organisms are grouped according to similarities derived from a common ancestry; those that share a common evolutionary heritage are monophyletic.
B. Portraying Relationships Among Organisms
1. A phylogeny is a pattern of evolutionary relationships and is somewhat hypothetical.
a. It depends on identification of homologous structures, which are features that can be attributed to a common ancestry.
b. A cladogram with its branching lines shows the relative relationships between organisms.
2. The determination of relative relationship is made by comparing the morphological, physiological, and behavioral characters of an “out-group” and the “in-group.”

V. Classification
A. Classification as a Retrieval System
1. A classification scheme provides useful information about the relationships among organisms.
2. The classification hierarchy in use today consists of: kingdom >> phylum (or division) >> class >> order >> family >> genus >> species.
3. The species is the only real entity in the schemes; all others are merely categories of relationship.
B. Five-Kingdom Classification
1. The widely adopted five-kingdom system was originated by Robert Whittaker.
2. The five kingdoms are:
a. Monera: single-celled prokaryotes (bacteria)
b. Protista: single-celled eukaryotes, some photosynthetic
c. Fungi: multicelled heterotrophs that feed by extracellular digestion and absorption
d. Plantae: multicelled photosynthetic autotrophs
e. Animalia: diverse multicelled heterotrophs



Chapter 21 The Origin & Evolution of Life
I. Life Begins
A. Evolution of life has been linked, from its origin to the present, to the physical and chemical evolution of the earth.
B. Origin of Life
1. Early Earth and Its Atmosphere
a. Planets formed about 4.6 billion years ago.
b. By 4 billion years ago, the earth’s atmosphere (no oxygen) was forming, liquid water was being retained by gravity, and primitive living cells were emerging.
c. Is it possible to devise experiments that would test whether life could have originated spontaneously under primitive earth conditions?
2. Synthesis of Biological Molecules
a. Components for building biological molecules accumulated in the primitive earth; and energy (lightning, heat) was present.
b. Stanley Miller used a lab apparatus to demonstrate synthesis of amino acids from hydrogen, methane, ammonia, and water under abiotic conditions.
3. Self-Replicating Systems
a. From accumulated organic compounds emerged replicating systems consisting of DNA, RNA, and proteins.
b. Clay particles may have first served as templates to assemble amino acids into proteins with enzymatic activity.
c. Ribonucleotides may have then stuck to the clay or amino acids, and eventually replaced clay as a template.
d. How DNA entered the picture is not yet clear, but we do know that some reactions were more probable than others—not random.
4. The First Plasma Membranes
a. The metabolism in living cells cannot occur without a barrier against the chemical actions on the outside.
b. The first cells were probably membrane-bound sacs containing nucleic acids that served as templates for proteins.
c. Sidney Fox heated amino acids to form protein chains, which when allowed to cool self-assembled into small spheres that were selectively permeable.
C. Drifting Continents and Changing Seas
1. Plate tectonics refers to the arrangement of the earth’s lithosphere in slablike plates that are in motion.
2. Continents have collided and split during the earth’s history.
a. Gondwana was the continent of the Paleozoic.
b. Pangea was the later continent that extended from pole to pole, then began breaking up during the Mesozoic.
3. When the land masses separated, speciation proceeded; when the land masses collided, diversity declined.

II. The Geologic Eras and Life
A. The Archean and Proterozoic Eras
1. Archean era (3.7 to 2.5 billion years ago) was the time of macromolecule synthesis plus the origin of anaerobic and photosynthetic cells (prokaryotes).
2. In the Proterozoic era (2.5 billion to 700 million years ago), photosynthetic bacteria and eukaryotic cells (algae, fungi) were abundant, oxygen accumulated, and aerobic respiration evolved.
B. The Paleozoic Era
1. During the Cambrian period, nearly all of the major phyla evolved; most organisms lived on or near the sea floor (trilobites were a dominant group).
2. In the Ordovician period, the Gondwana continent drifted southward, shallow marine environments were formed, reef organisms flourished, and glaciers formed to trigger the first mass global extinction.
3. In the Silurian and Devonian periods, Gondwana drifted northward, reef organisms recovered, predatory fishes flourished, and amphibians and stalked plants were moving onto land.
4. In the Carboniferous period, major radiations of plants and animals occurred as land masses were alternately flooded and drained; coal deposits formed.
5. In the Permian period, insects, amphibians and reptiles flourished; formation of Pangea supercontinent caused greatest of all mass extinctions.
C. The Mesozoic Era
1. In the Triassic period, mammals originated—small and few in number.
2. In the Jurassic period, dinosaurs emerged as rulers.
3. In the Cretaceous period, flowering plants emerged, overwhelming the gymnosperms; dinosaurs became extinct.
D. The Cenozoic Era
1. Major changes in land mass configurations, climates, and adaptive zones occurred.
2. Major adaptive radiation activity set the stage for major extinctions.