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AP Biology, Chapter 25
Tracing Phylogeny
Summary
Introduction
1. Distinguish between phylogeny and systematics.
a. Phylogeny is the evolutionary history of a group
b. Systematics is the study of biological diversity in an evolutionary context
THE FOSSIL RECORD AND GEOLOGICAL TIME
Introduction
Sedimentary rocks are the richest sources of fossils
2. Describe the process of sedimentation and the formation of fossils. Explain what
portions of organisms mostly fossilize and why.
a. Process
i. Minerals and organisms settle in water
ii. Organic substances decay
iii. Minerals seep in and crystallize
b. Hard parts fossilize most: decay/dissolve more slowly, or not at all
Paleontologists use a variety of methods to date fossils
3. Distinguish between relative dating and absolute dating.
a. Relative dating
i. By position in the rockpile
ii. Superposition: deeper, older; shallower, younger
b. Absolute dating: in years based on isotopic analysis and half lives
4. Explain how isotopes can be used in absolute dating.
a. Assumes we know the starting ratio of isotopes
b. Assumes changes in the sample are due to radioactive decay alone
c. Current ratio is measured; half-life used to calculate time
d. Examples: C-14, K-40, U-238
e. Non-isotopic methods: racemization of L-amino acids
The fossil record is a substantial, albeit incomplete, chronicle of evolutionary history
5. Explain why the fossil record is incomplete.
a. Fossilization is rare
i. Organism had to be buried
ii. Remains had to remain undisturbed
iii. Small chance of exposure by erosion
iv. Small chance of being found
b. Slanted toward fossils of long-lived, abundant, widespread species
Phylogeny has a biogeographical basis in continental drift
6. Describe two dramatic chapters in the history of continental drift. Explain how those
movements affected biological evolution.
a. 250 million years ago; formation of Pangaea
i. Once isolated populations became mixed
ii. Habitat changes: less coastline, drier interiors
b. 180 million years ago: break up of Pangaea
i. Reinstated widespread geographical isolation
ii. Current biogeographical patterns are the result
The history of life is punctuated by mass extinctions followed by adaptive radiation of
the survivors
7. Explain how mass extinctions have occurred and how they affected the evolution of
surviving forms.
a. Cambrian (?): evolution of hard body parts, increased predation
b. Permian, 250 million years ago due to some combination of:
i. Environmental changes related to the formation of Pangaea
ii. Massive volcanic eruptions
iii. Possible impact
iv. Anoxic oceans
8. Describe the evidence related to the impact hypothesis associated with the Cretaceous
extinctions. Describe the hypothesized consequences of such an impact.
a. Evidence
i. Iridium-rich layer on top of the Cretaceous rocks
ii. Chicxulub; large crater of the right age
b. Consequences
i. Dust released blocked sunlight for years; photosynthesis blocked
ii. Minerals released caused acid precipitation
iii. Molten debris rained on North America
PHYLOGENY AND SYSTEMATICS
Introduction
Taxonomy employs a hierarchical system of classification
9. Distinguish between systematics and taxonomy.
a. Systematics is the study of biological diversity in an evolutionary context
b. Taxonomy involves the identification and classification of species
10. Explain how species are named and categorized into a hierarchy of groups.
a. Binomial
i. Capitalized genus, non-capitalized species name
ii. Underlined or in italics
b. Hierarchy groups organisms into larger, more inclusive categories
11. List the major taxonomic categories from the most to least inclusive.
a. Domain, kingdom, phylum, class, order, family, genus, species
The branching pattern of a phylogenetic tree represents the taxonomic hierarchy
Determining monophyletic taxa is key to classifying organisms according to their
evolutionary history
12. Distinguish between homologous and analogous structures. Explain why the similarity
of complex systems implies a more recent common ancestor.
a. Homologous structures are inherited from a common ancestor
b. Analogous structures
i. Due to independent adaptation to similar selective pressure
ii. = convergent evolution
Molecular biology provides powerful tools for systematics
13. Explain how nucleotide sequences and amino acid sequences can be used to help
classify organisms. Explain the advantages that molecular methods have over other
forms of classification.
a. Count the similarities: the more similar, the more closely related
b. Advantages
i. More objective and quantitative than comparing shapes
ii. Can reveal relationships between seemingly identical or seemingly
unrelated organisms
c. Examples
i. Protein comparisons of common proteins like cytochrome c
ii. Hybridization, restriction maps and sequencing of DNA
14. Explain how molecular clocks are used to determine the approximate time of key
evolutionary events. Explain how molecular clocks are calibrated in actual time.
a. Basis of use
i. Evolution of some proteins and DNAs is relatively constant
ii. Number of substitutions is proportional to the time since divergence
b. Calibrated by graphing the number of differences vs. known branch points
15. Explain how scientists determined the approximate time when HIV first infected
humans.
a. HIV evolves rapidly
b. Samples of known age were sequenced
c. Number of differences in sequence has been increasing
d. Projection back to zero differences suggests in 1930 strain M entered humans
The search for fossilized DNA continues despite recent setbacks: science as a process
THE SCIENCE OF PHYLOGENETIC SYSTEMATICS
Introduction
Phenetics increased the objectivity of systematic analysis
Cladistic analysis uses novel homologies to define branch points on phylogenetic
trees
16. Define the parts and describe the interrelationships within a cladogram. Explain how
a cladogram is constructed.
a. Parts and interrelationships
i. Evolutionary branches, or clades, are monophyletic
.Mono-: all descendents having a certain trait; Amniota
.Poly-: common trait but not from a common ancestor;
endotherms
.Para-: common trait, common ancestor, but not all
descendents; reptiles
ii. Branch points, or nodes, represent common ancestors
iii. Sequence of branching represents historical chronology
b. Construction
i. Make a character table characters vs. taxa
ii. The more common the character, the farther down the branch point
17. Distinguish between shared primitive characters and shared derived characters.
Compare the definitions of an ingroup and outgroup.
a. In placing two taxa on a cladogram
i. Shared derived characters were unique to their common ancestor
ii. Shared primitive characters predates that ancestor
b. Groups
i. Outgroup: species somewhat related to the group under study
ii. Ingroup: the more closely related group under analysis
18. Compare the cladistic and phylocode classification systems.
a. Cladistic classification retains and creates taxon names
b. Phylocode includes only the clades with imposing hierarchical levels
19. Explain the principle of parsimony. Explain why any phylogenetic diagram is viewed
as a hypothesis.
a. Parsimony favors the simplest explanation consistent with the facts
b. Phylogenetic trees are hypotheses
i. Characters may later be shown to be analogous
ii. More characters might suggest a different branch pattern
Phylogenetic systematics relies on both morphology and molecules
20. Describe an example of a conflict between molecular data and other evidence, such
as the fossil record. Explain how these differences can be addressed.
a. Origin of major mammalian orders
i. Molecular clocks indicate divergence 100 mya
ii. Fossil evidence gives 60 mya
b. Orders might have originated 100 mya but became common 60 mya