I. Assigning Scientific Names
A. Why not use common names?
1. Differ from language to language
2. Differ from place to place
3. Different names for same species. Same name for different species.
B. Binomial nomenclature
1. Two-part scientific name. a. Genus species or Genus species
1. Genus: a group of similar species
2. Species: group of individuals capable of producing fertile offspring a. Species name often an important trait or the organisms habitat
C. Classifying Species into Larger Groups
1. Scientists classify species into larger groups that have biological meaning a. Systematics: Science of naming and grouping organisms
1. These groups are often referred to as taxa
II. The Linnaean Classification System
Domain— Archaea and Bacteria (Prokaryotic) or Eukaryotic
Kingdom—According to textbook--Largest and most inclusive of Linnaeus’s taxonomic categories
Phyllum—2nd largest group. Organisms are different but share important characteristics. Classes are grouped into a phylum
Class—3 rd largest group—Similar orders are grouped into a class
Order—4 th largest group—Closely related families are grouped into an order
Family—5 th largest group—Several genera that share many similarities are grouped into a family
Genus—6 th largest group—See above
Species—Smallest group—See above

Modern Evolutionary Classification
I. Evolutionary Classification
A. Phylogeny—The study of how living and extinct organisms are related to one another
1. Goal of phylogeny—group species into larger categories that reflect lines of evolutionary descent, rather than overall similarities and differences.
B. Common Ancestors—Phylogenetic systematics places organisms into higher taxa whos members are more closely related to one another than two members of another group
1. Larger the taxa  farther back in time members shared commone ancestor
C. Clades—Group of species that includes a single common ancestor and all descendants of that ancestor, living and extint.
1. A clade must be monophyletic (has a single common ancestor and all its descendants
D. Cladograms—links groups of organisms by showing how evolutionary lines, or lineages branched from a common ancestor.
1. Diagrams which depict the relationships between different organisms.
2. By depicting these relationships, cladograms reconstruct the evolutionary history
(phylogeny) of the organisms.
3. Cladograms can also be called “phylogenetic trees”.
4. Cladograms are constructed by grouping organisms together based on their shared derived characteristics.
5. Example: See below in “Interpreting Cladograms”
E. Building Cladograms
1. Example a. Given these characters and organisms: b. STEP ONE: Draw a Venn diagram. Start with the character that is shared by all the organisms on the outside. Inside each box, write the name of the organism that have only that set of characters.
Placenta
Mammary glands
Two pairs of limbs
Vertebrae

c. STEP TWO: Convert the Venn diagram into a cladogram like so:
F. Derived Characters
1. Derived Characters—A trait that arose in the most recent common ancestor of a particular lineage and was passed on to its descendants a. Example: Retractable claws. This is a derived trait found in the clade Felidae b. NON Example: Having four legs is NOT a derived characteristic as lots of clades
(tratrapods, amniota, mammalia) have 4 legs.
G. Losing Traits
1. Ancestors of snakes had four limbs. Somewhere in the linage leading to modern snakes, the trait was lost.
H. Interpreting Cladograms
Derived character: like
FEATHERS is a trait shared by all members of a clade an only by members of that clade
Node: Point at which two groups branched off from each other. Represents point at which those two groups shared a common ancestor.
J . Clades and Traditional Taxonomic Groups
1. A clade includes an ancestral species all its descendants.
2. Some traditional groups are not valid clades a. Ex: Linnaean class Reptilia, not a clade as it did not include birds, which also descended from the same ancestor.
II. DNA Classification
A. Genes as derived characteristics
1. Wide variety share a number of genes

a. Ex: All eukaryotic cells have mitochondria, all mitochondria have their own genes
2. Genes mutate over time. Shared genes contain differences that can be treated as derived characteristics.
3. The more derived genetic characters two species share, the more recently they shared a common ancestor.
B. New techniques suggest new trees.
1. Analyzing DNA can provide evidence that some species are more closely related than previously thought. a. Ex: African Vulture and American Vulture were classified in the falcon clade. American vulture urinated on its legs to cool itself down via evaporation, this is a behavior that storks exhibit as well. Molecular analysis of DNA provided evidence that American Vulture shared a more recent common ancestor with the Stork than with the African Vulture.
On your OWN paper, make a construct a cladogram.
Construct a Cladogram: Problem 1
Procedure: Using the characters in the data table construct a Venn diagram and a cladogram, or phylogeneic tree.
I. Data Table
Character
Vertebrae
Earthworm Trout Lizard Human
Legs
X X
X
X
X
X Hair
II. Venn Diagram
III. Draw a cladogram to illustrate the ancestry of these animals.

Building the Tree of Life
I. Changing Ideas About Kingdoms
A. Linnaeus’s two kingdoms (Animalia and Plantae) did not reflect full diversity of life
B. Before 1990 there were FIVE kingdoms
1. Monera a. Later this kingdom is divided into two different groups (Eubacteria and Archaebacteria)
2. Protista
3. Fungi
4. Plantae
5. Animalia
C. AFTER 1990 there are SIX kingdoms
D. Three Domains
1. Domain is larger, more inclusive than a kingdom
2. “Protista” is not a true clade as only monophyletic groups are valid under evolutionary classification. a. Consider them here as a group more for our convenience than as a reflection of close kinship b. Organisms classified as protists could be divided into 5 different clades
II. The Tree of All Life
A. The tree of life shows current hypotheses regarding evolutionary relationships among the taxa within the three domains of life.
B.
Domain Bacteria
1. Unicellular
2. Prokaryotic (lack membrane bound organelles)
C. Domain Arcahaea
1. Unicellular
2. Prokaryotic (lack membrane bound organelles)
3. Live in extreme environments a. Volcanic hot springs b. Brine pools c. Black organic mud totally devoid of oxygen
D. Domain Eukarya
1. Consists of all organism that have a nucleus

Domain Bacteria Archaea
Cell
Structures
Eukarya
Kingdom Eubacteria Archaebacteria Protista Fungi Plantae Animalia
Cell Type
Number of
Cells
Mode of
Nutrition
Examples
Student Notes

Patterns and Processes of Evolution
I. Speciation and Extinction
A. Macroevolutionary Patterns: Grand transformations in anatomy, phylogeny, ecology, and behavior which take place in larger clades than a single species
B. Macroevolution and cladistics
1. Fossils are classified using cladistic techniques. a. Based on shared or derived characteristics b. Fossils can be placed in clades that only contain extinct organisms or in clades that include living organisms.
C. Adaptation and Extinction
1. Organisms face changing environments a. Some species adapt and thrive b. Some species fail to adapt and become extinct
2. If the rate of speciation in a clade is equal to or greater than the rate of extinction, the clade will continue to exist. a. Example: Clade Reptilia includes snakes, lizards turtles, crocodiles, and dinosaurs. Most species in Clade Dinosauria went extinct but the clade itself survived as new species adapted to changing conditions. These new species are birds.
3. If the rate of extinction in clade is greater than the rate of speciation, the clade will eventually become extinct
D. Patterns of Extinction
1. Background Extinciton—Species become extinct due to slow steady process of natural selection.
2. Mass Extinction—Species becomes extinct over a short period of time. a. Terrestrial causes (Volcanic eruption) b. Extraterrestrial causes (Asteroid hitting Earth)

II. Rate of Evolution
A. Gradualism— idea that change occurs in a slow but continuous process
B. Punctuated Equilibrium--long periods of no change interrupted by relatively brief periods of sudden change
C. Rapid Evolution after Equilibrium
1. May occur after a small population becomes isolated from main population
2. May occur when small group migrates to new environment
III. Adaptive Radiation and Convergent Evolution
A. Adaptive Radiation—Process by which a single species or a small group of species evolves over a relatively short period of time into several different forms that live in different ways.
1. Example: Galapagos Finches

B Convergent Evolution—Type of evolution that produces similar structures and characteristics in distantly related organisms.
C. Coevolution—Process by which two species evolve in response to changes in each other over time.
1. The relationship between 2 coevolving species often becomes so specific that neither organism can survive without the other, thus an evolutionary change in one is followed by a change in the other
2. Example #1: Flowers and pollinators
3. Example #2: Plants and Herbivorous insects