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