A. Evolution is genetically-based change in a population over time. (Darwin called evolution "descent with modification").

B. Individual organisms DO NOT evolve.

C. Microevolution - relatively minor, genetically-based changes in a population over a relatively short period of time.

D. Macroevolution - relatively major, genetically-based changes in populations over a relatively long period of time.

1. Speciation - the evolution of new species from previously existing species.
2. What is a species?
a. biological species concept
b. evolutionary species concept

E. What is the ultimate source of the variation among organisms?

1. Changes in the gnome-mutations

F. Which mechanisms act on available variation to cause evolution to occur?

1. natural selection - differential success in the reproduction of different phenotypes resutling from the interaction of organisms with their environment.
2. genetic drift - changes in a small population's allele frequencies due to chance

G. Evidence - why do scientists think evolution is occuring and has occured?

1. observation - evolution has been observed many times.

a. peppered moths
b. guppies
c. resistance of bacteria to antibiotics that used to kill them
d. resistance of mosquitos to insectisides that used to kill them
e. many lab experiments with bacteria and viruses
2. artificial selection - farmers and other humans have selectively bred many species of organisms and purposely changed the species' attributes over time.
a. Canis familiaris (domestic dog)
b. corn
c. a species of wild mustard
- kale
- broccoli
- cabbage
- cauliflower
- etc.
3. anatomy and physiology of living species
a. vertebrate heart (# of chambers)
- fishes - 2
- amphibians, most reptiles - 5
- birds, mammals, few reptiles - 4
b. vertebrate brain
c. long, slender, forked tounge in snakes and some lizards
4. vestigial features
a. flightlessness in a number of bird species (example = flightless cormorant of Galapoagos Islands)
b. human cecum
c. eyes in many troglodytic and burrowing species (e.g., some fish, salamanders, naked mole rat)
d. pelvis in some snakes
5. metabolism of living species
a. glycolysis - used by virtually all living cells
6. development of living species
a. early-stage embryos are very similar among vertebrate classes
b. amniotic egg in reptiles, birds, and mammals
c. many aspects of evolution that seem improbable or even impossible cam be observed during development
- "ontogeny recapitulates phylogeny" - Hackel's biogenic law (not correct)
- caution: clearly development is not the same thing as evolution
7. behavior of living species
a. parental care and nest-building in crocodilians and birds
b. long-term parental care in humans and other primates
8. geographic distribution of living species
a. adaptive radiations on oceanic islands
b. similar but different species geographically isolated from each other
- ratite birds on the southern continents
9. fossils
a. transitional forms between early reptiles and mammals
b. Archaeopteryx
c. ancestry of horses
10. proteins
a. hemoglobin
b. cytochrome c
11. DNA

G. Charles Darwin and Alfred Wallace

1. independently arrived at the idea of natural selection
2. some common themes in their lives
a. among the greatest naturallists of all time
b. travelled/explored intesnsively
- Darwin - H.M.S. Beagle
- Wallace - South America, s.e. Asia
c. worked on islands
- Darwin - Galapagos
- Wallace - East Indies

H. Natural Selection

1. Selection acts on individuals, but its long term effect is on populations.
2. Selection acts on an organism's phenotype, which over time affects the population's genome.
3. example - peppered moths in England
4. determinants of phenotype
a. genotype
b. environment
c. traits affected by genes are inheritable
d. traits affected by environment only are not inheritable
5. adaptation - any feature of an organism that enhances its ability to survive and/or reproduce under its current environmental conditions
a. because environments change, a feature adaptive at time A may no longer be adaptive at time B
6. stabilizing selection
a. reduces variation
b. does not change mean
7. directional selection
a. changes mean in one direction
8. disruptive selection
a. favors the extremes in population over immediate forms
9. fitness - relative reproductive contribution of genotypes and their associated phenotypes
a. individual fitness - depends on relative number of offspring produced by an individual
b. inclusive fitness - depends on individual fitness and the survival/reproduction of an individual's close relatives
10. kin selection - a type of natural selection in which the relative contribution of a genotype is increased by "cooperation" among close relatives
a. scrub jays
b. eusocial species - include many sterile individuals
- many ants, bees, termites
- naked mole rat
11. sexual selection - a type of natural selection that favors traits which improve an individual's chances of mating
a. northern cardinal
b. bighorn sheep

Population Genetics

I. A population is a group of individuals of the same species living in the same area.

1. population charachteristics
a. size (number of individuals)
b. degree of isolation
c. gene pool - all the genes in a population at any time
d. genetic structure - the frequency of alleles and genotypes in a population
2. calculating allele and genotype frequencies; example:
a. a population has 500 members
b. white flowers - 10; pink 480
c. AA - 320; Aa - 160; aa - 20
d. How many alleles are in a population of 500?
e. What are the frequencies of A and a in the population?
- freq. of a = [(20x2)+(160x1)] / 1000 = 200 / 1000 = 0.2
- freq. of A = [(320x2)+(160x1)] / 1000 = 800 / 1000 = 0.8
- once we know the freq. of a, how else could we calculate the freq. of A?
f. What are the frequencies of the genotypes in the population?
- freq. of AA = 320/500 = 0.64
- freq. of Aa = 160/500 = 0.32
- freq. of aa = 20/500 = 0.04

J. Hardy-Weinburg Theorem

1. The frequencies of alleles and genotypes in a population's gene pool remain the constant over generations unless acted upon by asents other than sexual recombination.
2. Hardy-Weinburg equilibrium
a. A population is said to be at H-W equilibrium if its allele and genotype frequencies do not change from generation to generation
b. give criteria must be met for a population to be at H-W equilibrium
- very large population
- random mating
- no selection
- no immigration or emmigration
- no mutation
c. p+q = 1
d. p² + 2pq + q² = 1
e. p² + pq = p
f. q² + pq = q
3. If you know p, you can calculate q.
4. If you know q, you can calculate p.
5. If you know all genotype frequencies (AA = p², Aa = 2pq, aa = q²), you can calculate p and q.
6. If a population is at H-W equilibrium, you can calculate all genotype frequencies from p or q.
7. If a population is at H-W equilibrium you can calculate p, q, and all genotype frequencies by counting the number of individuals with the recessive phenotype.
8. Probability rules are behind H-W Theorem
a. freq. of A = p, so the probability that any fertilization event in the population involves a gamete with the A allele is p
b. so, the probability that both gametes involved in the fertilization event have the A allele is p² (rule of multiplication)
c. freq. of a = q; probability of getting aa is q²
d. probability of getting Aa involves rule of multiplication and rule of addition; pq + pq = 2pq
9. What can we conclude if a population is not at H-W equilibrium?
a. genetic drift (large population)
b. nonrandom mating (random mating)
c. natural selection (no selection)
d. gene flow (no imm- or emmigration)
e. mutation (no mutation)
10. So H-W Theorem can be used to detect microevolution in a population
11. Changes in generation to generation at a single locus are sufficient for saying that the population is evolving.
12. determining population size
a. effective population size - only breeding individuals are counted
13. nonrandom breeding
a. assortative mating - individuals choose mates with phenotypes similar to their own
b. inbreeding - individuals mate with relatives
c. results in increased homozygosity
d. by itself changes genotype frequencies, but not all allele frequencies

K. Genetic Drift

1. Drift can be defined as random changes in allele frequencies over time within a population.
2. Over time genetic drift can lead to the loss of some alleles and the fixation of others.
3. bottleneck effect
a. occurs when a population's numbers are drastically reduced
b. due to chance, allele frequencies in he surviving population will most likely differ from allele frequencies in original population
c. sampling error
4. founder effect
a. occurs when a small propagule colonizes a new area that is isolated from the rest of the population
b. same effect as bottleneck
c. sampling error

L. Additional notes on variation in populations and species

1. polymorphism - 2 discrete forms of the same trait exist in the population
2. geographic variation - individuals of a wide-ranging species may differ genetically and phenotypically from region to region
a. sometimes geographic variants are described as subspecies or races
b. geographic variation may occur over a short distance (e.g. on mountains)
c. cline - a slight difference that increases in degree from one end of a species' range to the other
3. diploidy allows harmful alleles to persist in a population
4. heterozygote advantage can help maintain the presence of 2 alleles at the same locus
a. sickle-cell anemia in populations exposed to malaria
b. hybrid vigor - crossing two inbred lines can result in more healty offspring
5. source variation - mutation
6. major increase in variation - recombination
a. not only are individuals unique because they have different alleles, they are unique because they have different combinations of alleles
b. random assortment
c. crossing over
d. sex
7. The less time required for individuals of a population to develop and reproduce, the faster variationcan accumulate in that population.

M. Speciation - the evolution of new species from formerly existing species

1. Allopatric specitation - speciation resulting from physical geographic separation of two or more populations
a. gene flow is physically prohibited
b. vicariance - a large population is divided into two or more parts by a barrier that arrises in the midst of the population
- examples - formation of mountains or canyons, a river changing its course, a large lake drying, climatic changes can fragment suitable habitat over time, continiental drift, etc
c. dispersal - a propagule colonizes an area that is remote from the rest
- flight
- rafting - some organisms can float across vast expanses of ocean on vegitation mats or just in the water
- hitchhiking - parasites, seeds, etc. can be transported by other organisms
- weather may be important
d. Both dispersal and vicariance can be observed in the modern world.
- numerous found out of range all the time (RBA's, etc.)
- rafting frequently observed after hurricanes, monsoons
- volcanic activity
e. Past vicariant events an past climatic conditions can be studied.
- geology
- palynology - study of fossil pollen
- paleontology - study of fossils
f. Some organisms are better dispersers than others.
- example very few amphibians found on oceanic islands
g. Small, peripheral isolates may be more likely to become new species.
- gene pool of peripheral isolate probably differs from gene pool of "parent" population (due to clines and/or founder effect)
- genetic drift will have an important effect until the peripheral isolate increases its numbers
- natural selection may have different effects on peripheral isolate due to environmental differences at the periphery of a species range (Why is a species' range the size it is?)
- many peripheral isolates may die out instead of speciating
- peripheral isolates may become reconnected to the parent
h. Which processes allow an isolated population to become a new species over a long period of time?
- genetic drift
- natural selection
- mutation
i. adaptive radiation
- on groups of islands (archipelago)
- following major extinction events
- occurs at a time or place with few competitors (lots of open niches)
2. Sympatric speciation - a new species originating within the midst of the parent population
a. "instant" speciation due to polyploidy
- autopolyploids - have more than 2 chromosome sets all derived from a single species
- allopolyploids - have more than 2 chromosome sets due to hybridization between two species
b. disruptive selection + associated mating
c. different habitat selection (e.g., Rhagoletis - hawthorn berries vs apples)
d. common in plants, rare in animals
3. Cladogenesis - a new species diverging from an existing species; the existing species continues to exist
4. Anagenesis - a single species changes over time so that it is different from its ancestors

N. Reproductive Isolating Mechanisms

1. Prezygotic barriers - impede mating or fertilization
a. habitat isolation - 2 species use different habitats (e.g., aquatic vs. terrestrial)
b. behavioral isolation - 2 species have different mating ritutals or signals (e.g., fireflies)
c. temporal isolation - 2 species breed at different times (e.g., summer vs. winter)
d. mechanical isolation - 2 species mah not be anatomically compatible (e.g., plants with different pollinators)
e. gametic isolation - the gametes of two species won't form a zygote (e.g., sperm won't live in female of other species; or chemical recognition of sperm by egg)
2. Postzygotic barriers - prevent hybrid zygote from developing into a viable, fertile adult
a. reduced hybrid viability - hybrid offspring are healthy but are also sterile (e.g., horse x donkey -> mule; mule is sterile)
b. hybrid breakdown - first generation hybrids are healthy and can reproduce, but their offspring are sterile or inviable

P. Recognizing species: theory vs. practice

1. theory - species concepts
2. practice - look for distinguishing features (and allopatry in many cases)
3. It is not always clear whether 2 populations represent the same species or not. Why might we expect to encounter this difficulty?
4. hybrid zone - narrow part of range where populations hybridize (e.g., red-shafted and yellow-shafted flickers)
5. Hypotheses are sometimes revised basd on new information (e.g., Tropidurus melanopleurs).
6. shifts in theory (lumpers vs. splitters; Baltimore vs. Bullock's orioles)

Q. Tempo of Evolution

1. phyletic gradualism - new species form slowly over large amounts of time by the accumulation of shift differences
a. Darwin
2. punctuated equilibrium - changes resulting in a new species can occur relatively rapidly and there may be very long periods of time during which species change very little
a. Eldredge and Gould (1972)
b. "relatively rapidly" may be on the order of 50,000 years or so
c. peripheral isolates
d. seems to be supported by fossil record
e. many phylogenetic studies seem to support it
f. adaptive landscape (Sewall Wright) could help explain evolutionary stasis
3. Gradualists and punctualists continue to debate the issue.
4. Both gradual and rapid change may be important in the history of life.

R. Phylogenetic Systematics

1. the study of the evolutionary relationships of species (phylogeny)
2. the classification of species according to their evolutionary relationships
3. monyphyletic groups are recognized with formal names (e.g., Paramecium, Felidae, Mammalia, Eukarya, etc.)
4. classification is revised so that paraphyletic groups are not recognized (e.g., Reptilia, Monera)
5. evidence from living and extinct species is used to make inferences about their phylogeny.
a. anatomy
b. development
c. behavior
d. life history
e. proteins
f. DNA, RNA
6. In cladistics, parsimony analysis is used to evaluate the evidence that is gathered.
a. synapomorphies (shared, derived characheristics) are considered evidence of relationship
b. ingroup
c. outgroup
7. Other methods may be used (e.g., phenetics, maximum liklihood).
8. Phylogenetic studies are important for many areas of biology
a. any study that makes comparisons among species
b. ecology
c. physiology
d. biogeography
e. epidemiology
f. conservation biology
g. etc.