1
Q
What 5 “sub-theories” does Ernst Mayr claim Darwin’s Theory of evolution is composed of?
A
- Evolution as such
- Common descent
- Multiplication of Species
- Gradualism
- Natural Selection
2
Q
What scale did Darwin stress that natural selection occurs at?
A
The organismal level
3
Q
What contraints might channel evolution?
A
- Structural
- Developmental
4
Q
Macroevolution
A
The study of the processes that cause biological lineages to split and the historical patterns that result from those splits.
- Lineages may consist of protein domains, tissues, species, or any other level of biological organization.
5
Q
What two points does Steve Gould focus on within Darwinism?
A
- Gradualism
- Natural Selection
6
Q
Hardy-Weinberg Equation
A
p2 + 2pq + q2
(When assumptions are met)
7
Q
What are the major deviations from the Hardy-Weinberg Hypothesis?
A
- Natural Selection
- Gene Flow
- Genetic Drift
8
Q
What are the consequences of gene flow?
A
Homogenize populations
- Homogeneous populations exchange alleles.
- Heterogeneous populations are isolated from each other.
9
Q
Genetic Drift
A
The change in the frequency of a gene variant (allele) in a population due to random sampling.
10
Q
What are the four postulates of natural selection?
A
- Individuals vary
- Some variation is heritable
- Not all individuals survive
- Differential fitness
11
Q
What are some common misunderstandings of natural selection?
A
- Selection acts of individuals, though the consequences are seen in populations
- Selection acts on phenotypes but microevolution is the change in gene frequencies.
- Natural selection is not forward looking.
- Natural selection acts on existing traits.
- Natural selection is not random.
- Fitness is not circular (it is a statistical process).
12
Q
What are two general ways to measure “evolutionary time”?
A
- Fossil/Stratigraphic record approximates evolutionary time
- Phylogeny
13
Q
Operational Taxonomic Unit (OTU)
A
Complicated term for the name of a species at the end of a phylogenetic branch.
14
Q
Polytomy
A
More than two branches stemming from a single node.
15
Q
Trichotomy
A
A special type of polytomy involving three branches stemming from a single node.
16
Q
Cladogram
A
A phylogeny in which branch lengths have no meaning.
17
Q
Phylogram
A
A phylogeny in which branch length is proportional to change.
18
Q
Ultametric Phylogram
A
Branch lengths are proportional to change or time (tips / leaves are at the same point)
19
Q
Ancestral State
A
Any characteristic shared between one or more species and a common ancestor.
20
Q
Why are phylogenetic trees used in biogeography?
A
To reconstruct the history of where species have lived.
21
Q
Parsimony
A
A criterion used for creating phylogenies, where the fewest number of changes during evolution is the favored explanation.
22
Q
Dollo’s Law
A
Complex characteristics are usually assumed to evolve the same way only one time.
- Exceptions (multiple origins of complex traits) indicate interesting evolutionary traits.
- One exception is that some distantly related fish have placentas (a complex trait whereby the mother nourishes her unborn young).
23
Q
What are the five main uses of phylogenetic trees?
A
- Biogeography
- Ancestral State Reconstruction
- Tempo of evolution / timing
- Correlated Evolution
- Measure Biodiversity
24
Q
Felsenstein Zone
A
Conditions under which parsimony is “positively misleading”.
25
What are three important ways used to test for phylogenetic methods?
1. **Congruence**: Do the procedures agree among different datasets?
2. **Known Phlogenies:** Well supported or experimentally generated.
3. **Simulations**: Generate data with a computer.
26
Stromatolite
Rock-like structure found in shallow waters that are formed, layer upon layer, by the waste products from microorganisms such as cyanobacteria.
* Provide some of the most ancient records of early life on Earth.
27
Trace Fossil
Geological records of biological activity whereby impressions of footprints or some other biological marker indicates the existence of a specific organism at a point in time deterimined by te rock layer at which it is found.
* In the broadest sense it can include organism byproducts such as stromatolites.
28
Name five major uses for phylogenies.
1. Biogeography: the estimation of where organisms lived in the past based off of phylogenetic relationships of known species.
2. Ancestral State Reconstruction
3. Tempo of Evolution
4. Correlated Evolution: Correlation between traits and environment taken as evidence for “adaptation”
5. Measure Biodiversity
29
What are the four postulates of natural selection?
1. Variation occurs within a population
2. Some of the variation is heritable
3. Not all organisms survive to reproduce
4. Survival is non-random w/respect to traits
30
Which nucelotides are the purine and which are the pyramidines?
Purines = Adenine And Guanine
Pyrimidines = Cytosine and Thymine
31
Transition Mutation
Within purines or pyrimidines exlusively.
32
Transversion Mutation
Between purines and pyrimidines.
33
Synonymous Substitution
A mutation that doesn't change the amino acid produced.
Called either Ks or ds
34
Non-Synonymous Substituion
A mutation that *does* change the amino acid produced.
Either called Ka or dn
35
Purifying Selection
When mutations that change the amino acid are purged (selected against).
36
Positive Selection
When mutations that change the amino acid produced are favored (selected for).
37
Under neutral evolution, Ka/Ks = ?
38
How is the molecular clock theory used in modern evolutionary science?
The clock is often tested as a null model--if not rejected then used as an assumption.
39
What are three factors that can potentually modulate the molecular clock?
* Mutation rate (repair efficiency)
* Generation time
* Metabolic rate
40
Gene Family
A family of related genes within one or more genomes. The level of relatedness is subjective.
41
Gene Duplication
Physical duplication of a stretch of DNA, producing two (initially) identical sequences in the genome.
* Can occur at a range of scales from a few bases to the entire genome.
* Various possible mechanisms.
42
What are the three main mechanisms for gene duplication?
1. **Retrotransposition**: reverse transcription and integration.
2. **Segmental**: unequal crossing over through paralog recombination causes a tandem duplication event.
3. **Segmental (non-homologous)**: a replication error causes a tandem duplication event.
43
Allotetraploidy
Genome duplication event whereby an individual with a hybridized genome is produced.
44
Autotetraploidy
Genome duplication event whereby an individual with a duplicated genome is produced.
45
\_\_\_\_\_ vision refers to that seen mainly through the rods in dim light situations, whereas _____ vision refers to that seen chiefly through the cones in bright light situations
Scotopic; photopic
46
Dichromat Vision
Having two cone opsins in eyes--most mammals have this vision.
47
Orthologous
Term used to denote speciation events within a phylogeny.
48
Paralogous
Term used to denote a duplication event with a phylogeny.
49
Inference of function is best made between _____ sequences.
orthologous; paralogues may have different function.
50
What are Non-, Neo- and Sub-functionalization?
Possible outcomes following gene duplication.
1. _Non-functionalization_:
* Deleterious mutation in one gene, which subsequently becomes a *pseudogene.*
2. _Neo-functionalization_:
* One gene retains old function while another obtains new function.
* Classic model of gene duplication evolution.
3. Sub-functionalization:
* Assumes ancestral gene had multiple functions.
* Descendent genes divide up function of ancestral genes.
51
Is Neutral theory considered Darwinian?
52
What is three qualities are necessary for natural selection to act?
1. Variation
2. Heritability
3. Biased survival with respect to heritable variation.
This is true among all levels of biological organization.
53
Evolutionary Altruism
Behavior that increases the fitness of the recipient at the expense of the donor.
54
As many as __ jays help raising the young of a breeding pair.
55
What are four pieces of evidence that support endosymbiotic theory for mitochondria and chloroplasts?
1. Mitochondria and chloroplasts arise only from preexisting mitochondria and chloroplasts.
2. Mitochondria and chloroplasts have their own genome.
3. Organelles have their own protein-synthesizing machinery (e.g., tRNA's, rRNA's).
4. Phylogenies
56
What bacteria are mitochondria most closely linked to?
Ricketssia
57
How did August Weismann disprove Lamarkian Evolution?
He cut off the tails of 22 generations of mice and found that each successive generation retained their tails.
58
Soma
The term used to describe the body of an organism--what befalls these cells is not passed on to offspring.
59
Germ-line
Tissues that produce gametes and are responsible for genetic heritability.
60
What occurs when the regulation of cell differentiation among multicellular organisms breaks down?
Cancer
61
What three factors drive evolution?
Structure, function and history.
62
What are the three ways to test for adaption?
1. **Optimality**: estimate an optimal phenotype based on some prediction and see if the organism matches the optimal.
2. **Experimentation**: experimentally manipulate a trait and look for adaptive (survival or reproductive) differences.
3. **Comparative Method**: look for correlations across species independently of phylogenies.
63
What is the Adaptionist Programme?
Proceeds in 2 steps:
1. Separate an organism into individual "traits".
2. Interaction between traits is only secondarily recognized.
* Trade-offs force sub-optimality.
* Sub-optimality of one part is only to benefit the optimality of the whole.
64
What are four common arguments of Adaptionist Program followers?
1. If one adaptive argument fails, move on to the next.
2. If one adaptive argument fails, assume another must exist.
3. Absence of good adaptive argument indicates lack of knowledge (e.g., Wallace on snails).
4. Emphasize current utility and ignore other attributes of form (e.g., *T. Rex* front limbs)
65
What are Gould's and Lewontin's primary problem in accepting the adaptionist program?
They object to the *ad hoc* nature and believe that science must present testable hypotheses.
66
What are the leading hypotheses on why cavefish lose functional eyes?
1. No cost to loss, mutations accumulate
2. Developmental trade-off
* "Likely in relation to feeding preferences, cavefish have also increased the size of their jaws, the number of oral and pharyngeal tastebuds and the number of maxillary teeth"
67
What gene is hypothesized to be a "master switch" for eyes?
Pax-6
68
Atavism
To have reverted to an ancestral state.
* Demonstrates that genetic capability is not (always) lost when a structure is lost. Thus, N.S. is not all powerful.
69
Dollo's Law
Proposed in 1890, and states that if an organ or structure is lost, it will not be regained.
70
Switchback Evolution
A term coined by Van Valen that is used to describe scenarios whereby Dollo's Law is violated by functional atavisms.
71
Pleiotropy
Term for when a gene has more than one function.
* Lens crystallins are good example
* Enzymes are recruited into eye lenses as structural proteins.
72
Morphological change = _____ + \_\_\_\_\_?
genetic change; developmental change
73
Heterochrony
Evolutionary changes where a developmental process is UNIFORMLY sped up, slowed down, or has its onset or offset shifted in time.
74
Hypermorphosis
Development of the character in the descendent continues beyond the point at which it stopped in the ancestor.
75
Progenesis
Development of the character in the descendant stops earlier than it did in the ancestor.
76
Neoeny
The character develops at a lower rate in the descendant than in the ancestor.
77
Acceleration
The character develops at a higher rate in the descendant than in the ancestor.
78
Postdisplacement
The character begins developing later in the descendant than it did in the ancestor.
79
Predisplacement
The character begins developing earlier in the descendant than it did in the ancestor.
80
81
Adaptive Zone
A collection of empty niches that may be exploited by a set of species varying in phenotype but descended from a common ancestor.
* A set of niches that do not require major discontinuities in way of life.
82
Non-adaptive radiation
Rapid proliferation of species w/o ecological differentiation.
83
What are two primary causes of non-adaptive radiation?
1. Sexual selection causing diversification
2. Non-genetic associations with ecology--without adaption
84
What are Schluter's four criteria for adaptive radiation?
1. Common ancestry
2. Phenotype-environment correlation
3. Trait utility
4. Rapid speciation
85
Key Innovation
A novel trait that influences the ability to exploit previously unused resources.
86
Pseudoextinction
When a species has evolved into another species under a different name, but the lineage has not died out.
87
What is the minimum number of mass extinctions that our planet has experienced?
Nearly all scientist agree five, although there are those that argue for higher numbers under different definitions of the term.
88
What is the leading hypothesis for the cause of the K/T extinction and what is the supporting evidence?
The hypothesis is that a large meteor struct the earth and set the envrionmental conditions askew. Evidence comes from:
* Iridium (a common compound found on asteroids) spike at time of extinction.
* Yucatan crater 180 km in diamter dates back to K/T
* Shocked quartz
* Sink holes
* Sallelite images
89
Crown Groups
Term used to describe species within a clade in relation to a stem group, which is composed of extinct spcies that is a sister group to the crown group.
90
What factors deviate from the assumptions of the Hardy-Weinberg equilibrium?
1. Natural selection
2. Gene flow
3. Genetic drift
91
