Introduction
to Evolution
Students will
be able to:
- define biological evolution
- discuss evolutionary ideas before Darwin's book
was published
- describe how geological theorists' and Malthus's
ideas on population regulation influenced Darwin's conception of biological
evolution
- define Darwin's contributions
to evolutionary theory
- describe the reception Darwin's ideas received and competing evolutionary
ideas
- discuss the impact of Mendelism on evolutionary
thought and the controversy between the Mendelians and the Biometricians
- describe the the Modern Synthesis and the manner
in which it resolved the controversy
- discuss the interrelationships between molecular
biology, developmental biology, and evolutionary theory
Return to History
of Evolution Lecture Notes
Systematics
and Evolution
Students will
be able to:
- describe the concept of relatedness and its
connection to biological evolution
- differentiate between taxonomy and systematics
- define phylogenetics
- describe the roles that plesiomorphies, synapomorphies,
and autapomorphies have in detecting common ancestry
- define homoplasy, describe the forms that homoplasy
may take, and discuss it's relevance to phylogenetic reconstruction
- give an overview of how phylogenies are constructed
- describe and compare distance measures, parsimony,
likelihood, and Bayesian probability as criteria for comparing candidate
phylogenies
- explain why heuristic searching is a necessary
compromise
- describe the mechanism behind molecular clocks
for phylogenetic reconstruction and the potential problems with their use
- explain the purpose and mechanism of the relative
rates test
- describe the problems for phylogenetic reconstruction
that incomplete lineage sorting, character scoring, long-branch attraction
and base composition bias present
- define reticulate evolution and explain how
hybridization, horizontal gene transfer and gene duplication produce reticulate
evolution
- distinguish parallelisms from convergences and
explain how both are sources of homoplasy
- define reversals and explain how it produces
homoplasy
Return to Systematics
Lecture Notes
Some
Basic Patterns in Evolution
Students will
be able to:
- discuss the merits of branching versus hierarchical
classification
- compare ancestry to phenetic similarity as a
basis for systematic classification
- discuss the evidence for evolution through cladogenesis
- discuss the evidence for evolution through natural selection
- define modular development and individualization
- explain the role that heterochrony may play
in creating both within- and between-species phenotypic variation
- define paedomorphosis and peramorphosis
- define allometry and explain the allometric
growth equation
- linearize the allometric growth equation
- describe the means by which allometry may produce
paedomorphosis and peramorphosis
- define heterotopy
- compare orthologs to paralogs and discuss the
problems produced by the latter in phylogenetic reconstruction
Return to Basic
Patterns Lecture Notes
Lecture
04Evolution, Geology, and the Fossil Record
Students will
be able to:
- distinguish among igneous, metamorphic and sedimentary
rocks
- define fossil and describe the types of fossil
- describe how plate tectonics shapes the surface
of the globe using appropriate terms
- compare relative to absolute dating of rocks
- describe the geological time scale in both relative
and absolute terms
- explain how radioactive isotopes are used to
date rocks
- name the eons, eras, periods and Cenozoic epochs
and give approximate dates for the beginning of each
- give the relative age of the first appearance
of prokaryotes, invertebrates, land plants, jawed fish, land plants, land
vertebrates, mammals, and flowering plants
- give the relative age of the expansions or radiation
of oxygen in the atmosphere, jawed fish, forests; reptiles, flowering plants,
and mammals
- discuss the quality of the fossil record
- discuss the origins of Amphibia, birds, mammals
and hominids
- define "evolutionary trend" and "evolutionary
rule"
- describe Dollo's law and its importance to reconstruction
evolutionary histories
- discuss how phylogenetic burden might explain
some of the linkage between development and phylogenetic history
- distinguish between punctuated equilibria and
phyletic gradualism as models of the evolutionary process
Return to Evolution,
Geology, and the Fossil Record Lecture
Notes
Lecture
05Evolution and Geography
Students will
be able to:
- define biogeography and explain its relationship to evolution
- distinguish
between endemic and native species
- define autochthonous and allochthonous species
- describe the biogeographic realms
- distinguish between disjunct and relict populations
- describe how extinction, dispersal, and vicariance affect species distributions
- define phylogeography
- explain the niche and how the idea is used to explain species' range limits
- define phylogenetic niche conservation and describe the biogeographic patterns
produced by it
- define the latitudinal diversity gradient and discuss the historical hypotheses
suggested as explanations for it
Return to Evolution
and Geography Lecture Notes
Lecture
06Microevolution: Variation
Students will
be able to:
- describe the structure of genomes and genes
- describe gene mutations and their possible effect
on an organism's fitness
- describe chromosomal mutations and their possible
effect on an organism's fitness
- explain how mutation rate is measured and how
it differs among organisms
- relate randomness of mutations to genetic variation
- explain the effect of pleiotropy on the relationship
between mutation and fitness
- discuss the factors that lead to phenotypic
variation
- define norm of reaction
- explain the effect of recombination on genetic
variation
- explain why linkage disequilibrium is a measure
of the inhibition of recombination
- use Hardy-Weinberg equilibrium to predict genotype
frequencies
- discuss how and why evolutionary processes alter
Hardy-Weinberg expectations
- explain the relationship between phenotype (and
phenotypic variation) and genotype (and genotypic variation)
- define heritability
- define gene-by-environment interactions and
reaction norms
- describe clines and population structure
- explain why adaptive geographic variation is
at odds with gene flow
- describe countercurrent gradients and character
displacement
Return to Microevolution:
Genetic Variation Lecture Notes
Lecture
07Microevolution: Genetic Drift
Students will
be able to:
- explain why random processes are part of the
mechanism of evolution
- discriminate between adaptive and non-adaptive
evolution
- explain why the frequency of an allele in a
finite population is expected to fix at either 1.0 or 0.0
- define sample error and describe the effect
of sample size on the magnitude of sample error
- define deme and metapopulation
- describe the effect of population subdivision
on the rate of genetic drift
- describe the effect of genetic drift on genetic
diversity in general
- how do drift and recombination influence linkage disequilibrium
- describe the probability of fixation at 1.0
of an allele and the expected time until fixation
- define effective population size and explain
why it is always less than or equal to census population size
- define bottleneck and founder effects
- describe the neutralist-selectionist debate
- define the neutral mutation rate and explain
why some positions in a gene sequence are not expected to fix mutations
at the neutral mutation rate
- explain how the fossil record can be used to
calibrate the molecular clock, including the assumptions that must be met
- predict the proportion of heterozygotes expected
for loci under the neutral theory of evolution
- predict the migration rate from the variation
found at a locus
- contrast genetic drift and gene flow from migration
- describe the coalescent
- name the uses to which coalescent theory can
be applied
Return to Microevolution:
Genetic Drift Lecture Notes
Lecture
08Microevolution: Natural Selection
Students will
be able to:
- describe the assumptions of evolution through
natural selection
- define natural selection
- define adaptation and relate it to natural selection
- define fitness and relate it to both natural
selection and adaptation
- discuss goal-driven processes and evolution
- describe sexual selection
- compare and contrast natural and sexual selection
- explain the nature of conflict between natural
and sexual selection
- compare and contrast natural selection with
genetic drift
- describe means of differentiating between selection
and drift
- define hitchhiking in evolutionary terms and
relate it to natural selection and drift
- define a trade-off and explain its importance
to adaptation and natural selection
- define four levels of selection
- discuss genic selection
- describe selfish genetic elements and explain
why they represent genic level selection
- explain why the tailless locus in mice is an
example of a selfish genetic element
- define individual selection
- define kin selection and explain why it is an
example of individual selection
- define inclusive fitness and distinguish it
from the usual definition of fitness
- explain why haplodiploid sisters are more related
to one another than they are to their mother and sisters in non-haplodiploid
species
- describe group selection
- define an altruistic trait
- discuss the reasons to discount group selection
as an important evolutionary process
- discuss the reasons to count group selection
among the important evolutionary processes
- describe the group selection experiments using
Tribolium and explain why they supported group selection as an important
evolutionary process
- describe how species selection happens
- discuss constraints as alternative explanations
for phenotypic change
- define preadaptation and exaptation
- explain the ways one might determine if a trait
is the process of natural selection
- discuss the idea of progress in evolution
- discuss the natural fallacy
Return to Microevolution:
Natural Selection Lecture Notes
Lecture
09Microevolution: Modeling Evolution
Students will
be able to:
- draw and describe the three modes of selection
- define a balanced polymorphism
- define fitness and describe fitness components
- distinguish between relative and absolute fitness
- use data on the relative fitness and frequencies
of genotypes to calculate the mean population fitness
- describe the coefficient of selection and relate
it to relative fitness
- apply the discussed model of selection to predict
the change in frequency of the A1 allele for the two-allele
case under different fitness and dominance relationships
- describe how mutation and migration can produce
balanced polymorphisms
- explain balancing selection as a means of producing
a balanced polymorphism
- contrast and compare heterozygote advantage
and overdominance
- explain frequency-dependent selection as a means
of producing a balanced polymorphism
- describe adaptive landscapes and explain how
this idea may explain the occurrence of balanced polymorphisms
- define antagonistic selection
- explain why too many mutations in a gene sequence
indicates balancing selection and why too few indicates directional selection
Return to Microevolution:
Modeling Evolution Lecture Notes
Lecture
10Species and Speciation
Students will
be able to:
- distinguish
- discuss the importance of the species concept
- define and discriminate among biological, phylogenetic,
genealogical, cohesion, recognition, and evolutionary species concepts
- explain the relationship between the biological
species concept and reproductive isolation
- describe the modes of pre- and post zygotic
reproductive isolation
- explain the role of intraspecific variation
(genetic and phenotypic) in the generation of new species
- name, define the various kinds of genetic variation
and relate them to phenotypic variation and speciation
- explain the advantages Drosophila have as model
organisms and describe the genus.
- define epistasis and discuss its role in reproductive
isolation and speciation
- describe the origins of hybrid organisms, their
ecology, and their relationship to the biological species concept
- explain the processes that promote and prevent
speciation
- define and compare the modes of speciation
- discuss the roles of natural and sexual selection
in speciation
- discuss the effect of speciation on macroevolutionary
processes
Return to Species
and Speciation Lecture Notes
Lecture 11Evolution
and Sex
Students will
be able to:
- explain the origin of mutations and the concept of a mutation rate
- contrast the evolution of mutation rates in sexual and asexual organisms
- explain how canalization is an example of constraint
in evolution
- define terms that describe sexual systems: asexual
(amictic, apomictic), sexual (mictic), parasexual (transformation, conjugation,
transduction). recombination, suppression of recombination
(crossover), legitimate and illegitimate crossover, isogamy, aniosgamy, mating
type, sex, dioecious (gonochorism, bisexual), monecious, (unisexual, cosexual,
hermaphrodite
[simultaneous and sequential]), parthenogenesis,
vegetative reproduction
- explain the potential costs of sexual reproduction
- describe Muller's Ratchet and how sex affects
its operation
- explain why sex might be an advantage in fluctuating environments
- describe the rare sex advantage and why it predicts 1-to-1 sex ratios
- define local mate competition explain why it shifts the expected sex ratio
toward females
- describe the effect of a predictable rare sex on the expected sex ratio
- define sex allocation and predict allocation based on reproductive success
- define inbreeding depression and explain why it reduces genetic variation
- define outbreeding depression and how inbreeding reduces its cost
- define sexual selection and its relationship with anisogamy
- define sexual conflict
- explain male/male contests in terms of sexual conflict
- define sperm competition
- define mate choice
- explain how sensory bias, direct benefits or indirect benefits may result
in mate choice
- define runaway selection
- explain how mate choice can result in runaway selection
- explain how sexy sons may lead to runaway selection
- define coevolution and antagonistic coevolution
- explain how sperm competition can produce antagonistic selection between
sperm and egg
- explain how differences between the interests
of males and females can lead to antagonistic selection
- explain chase-away selection and how it might produce exaggerated male
phenotypes
- define a sneaky male
- explain the conditions that favor male-first
and male-last sequential hermaphroditism
Return to Sex and Evolution Lecture Notes
Lecture 12Conflict
in Evolution
Students will
be able to:
- define cooperation in an evolutionary sense
and explain why individual selection may oppose cooperation
- separate cooperation from altruism
- explain why group selection promotes cooperation
- explain the effect of cheaters on the evolution
of cooperative interactions
- define an evolutionary stable strategy
- describe the prisoner dilemma
- define kin selection and explain why it might lead to apparent altruism
- describe the manner in which direct benefits can lead to cooperation
- define manipulation and how it can result in
apparent altruism
- explain how reciprocation can lead to cooperation and altruism
- define biological promiscuity, polygamy, polygyny, polyandry, monogamy,
and pair-bonding
- explain how parental care can lead to conflict within the family
- define mating conflict and explain why it is
a source of antagonistic selection
- explain how parents and offspring can be in
evolutionary conflict
- describe the three general conflicts arising
from asymmetries in the evolution of parental care
- define siblicide and describe why it might be
favored by natural selection
- define genetic conflict, selfish genes, and
restorer genes
- explain the conflict between selfish and restorer
genes
- define genomic imprinting and why it is an example
of genetic conflict
- explain the difficulty of defining a biological individual presented by
the presence of endosymbionts
- place parasites, commensals and mutualists on
a cost/benefit continuum
Return to Conflict and Evolution Lecture Notes
Lecture 13Evolution
and Development
Students will
be able to:
- contrast Naturphilosophie and Entwicklungsmechanik
and relate them to the origins of developmental biology
- briefly discuss the importance of developmental biology to the adoption
of experimentation by biology
- describe the changes that lead to dropping the
name "embryology" and adopting the name "developmental biology"
- explain how canalization is an example of constraint
in evolution
- relate the major difference between population biologists and evo-devo
researchers
- define metamerism and relate it to modularity
- explain how modularity simplifies constructing complex organisms
- define homeobox, homeodomain and hox
- describe the structure, mechanism of action, and general effect of Hox
genes
- explain why all homeobox genes are not Hox genes
- relate homeobox to MADS-box genes
- explain the evidence for WGD in vertebrates and contrast it with local
duplication as a means of increasing genomic complexity
- explain why serial homologies are not synapomorphies
- define effector (structural) genes, transcription factors, enhancer sites,
signaling proteins, and receptor proteins
- define a developmental pathway
- explain why changes in developmental patterns
are more likely to be due to changes in regulation than to changes to effector
genes
- explain the general ways in which regulation of a developmental pathway
might change
- define exaptation, recruitment and co-option
- define the four kinds of evolutionary constraint
- explain how these constraints might result in
- a failure to evolve
- directional trends
- parallel evolution
- morphological stasis
- the similarity between ontogeny and phylogeny
Return to Evolution and Development Lecture Notes
Evolution
and Our Society
Students will be able to:
Return to Evolution and Society Lecture Notes
Microevolution:
Quantitative Traits
Students will be able to:
- define phenotypic traits
- discuss the relevance of artificial selection
to the study of quantitative traits
- explain why the midpoint is the expected heterozygote
phenotype
- define additive effects
- explain why dominance and additivity are mutually
exclusive
- describe (using diagrams) the response to selection
of a quantitative trait
- decompose phenotypic variation into its additive
components
- calculate the expected phenotypic variance due
to additive effects
- define narrow-sense heritability and describe
two ways to measure it
- define mapping markers
- describe how markers can be used to determine
the number of loci affecting a phenotypic trait
- discuss the drift of neutral phenotypes
- define correlated evolution
- contrast correlate selection with genetic correlation
- explain how pleiotropy or linkage disequilibrium
bring about genetic correlation
- explain the role modifier loci play in amelioration
pleiotropic phenotypic effects
- define a norm of reaction and relate a norm
to phenotypic plasticity
- discuss the impact that reaction norms may have
on development
- define canalization and explain its importance
Return to Microevolution: Quantitative Traits
Lecture Notes
The Compleat Cladist: How to do Basic Phylogenetics
Students will be able to:
- define phylogenetic terms related to groups
of organisms, characteristics of organisms, relationships among organisms
and classification
- use parsimony to construct a simple phylogenetic
tree
- root a tree using an outgroup
- use the Henning and Wagner algorithms to construct
trees
- determine ancestral states using ACCTRAN
Return to Lecture Notes