Lecture 1: 

What is the difference between catastrophism and uniformitarianism?

Cuvier pioneered the theory of catastrophism, which stated that the extinctions happened as a result of violent geological events such as earthquakes and massive volcanic eruptions.

Hutton advanced the theory of uniformitarianism, which stated that mountains and river valleys had been formed by gradual processes, such as the deposition of sedimentary material that was hardened by heat and pressure into rocks. 

Lecture 1:

How did Lamarck incorporate the giraffe example into his theory of evolutionary change? 

Lecture 1:

What was significant about Darwin's phylogenic tree which described the relationship among the 13 species of finches on the Galapagos Islands?

Lecture 1:

What is the Malthusian Principle?

Malthus stated that the human population grows exponentially while the resources necessary for our surivial grows linearly/arithmetically. The exponential growth of the human race will inevitably outstrip the arithmetic growth of land available to support them. The result will be famine,warfare, and disease which will keep the population in check and the cycle will repeat itself. 

It describes the divergence between the exponential growth of a population and the arithmetic growth of resources such as land for crops. 

Lecture 1: 

List the characteristics of Darwin's theory.

1. Members of a species vary in their characteristics.

2. At least some phenotypic variation must be heritable.

3. Natural Selection can give rise to new adaptations and new species.

4. Natural and Artificial Selection are similar but not identical

Lecture 1:

Why was Mendel's experiment significant

It confirmed that inheritance is particulate and alleles of genes are passed monstly unchanged from one generation to the next. These alleles are recombined in a random way so that the offspring are not simply exact copies of their parents. Mendel used Pisum Savitum pea species in his crosses.

Darwin assumed that inheritance occurred through blending, which means that half of the phenotypic variation disappears each generation. Mendel's inheritance mechanism allowed genetic variation to persist for many generations, which could by acted on by natural selection at any time. 

Lecture 1:

What was significant about the Daphne Major , Geospiza fortis finches? What was the gene involved?

During a drought, these finches survived because they had larger bills/beak sizes that enabled them to crack the large seeds of the surviving plants. The beak sizes of the parents and offspring are correlated so that there was a genetic component to the beak size during the drought. This isn't because of environmental change, but because of genetic variation contributing to this phenotypic change. If it were because of environmental change, then there would be no correlation between the mean bill depth of parents and offspring. 

BMP4 gene, a gene coding for bone morphogenesis protein, was expressed strongly in finches with larger beaks. The Grants and their colleagues were able to show that natural selection has brought a change in the genetic makeup of the finch population but the exact genetic base of the change has to be determined. 

Lecture 1:

What is the difference between artificial and natural selection?

Lecture 2:

List the other 3 characteristics of Darwin's Theory

5. Evolution is gradual.

6. All present day organisms may be descended from a single ancestor 

7. Evolution leads to increased survival through adaptation. 

Lecture 2:

What is the difference between homologous characters and homoplasies?

Lecture 2:

Describe the monophyletic and polyphyletic terms.

If we are describing modes of reproduction:

If a placental mode of reproduction is a shared derived character, which means that all the placentals can be grouped together into a monophyletic clade, one with a single common ancestor. The placental reproduction in the different clades is homologous.

If the placental mode of reproduction arose more than once and the placental mammals on this tree have converged on this character, then the placental characteristic is polyphyletic, made up of more than one clade, and the placental reproduction in the different clades is analogous.

Lecture 2:

What is the difference between maximum parismony and relative likelihood?

A maximum parsimony tree obeys Ockham's razor because it requires the smallest overall # of events (less internal nodes, the more parsimonious; assume placental monophyly)

Relative likelihood looks to molecular data and corrected % differences (for homoplasy by the Kimura 2 parameter correction) to create a tree. The transition-transversion parameter was set by using the observation that in hemoglobin genes transition substitutions are twice as likely to take place as transversion substitutions when genes begin to diverge. The larger the molecular data set, the better the agreement of the tree with morphological and fossil data.

Lecture 2:

Describe mutations.

There are gene and chromosomal mutations, that are small changes in DNA molecules and shuffling of the order of genes on chromosomes (gain or loss) respectively. DNA pieces can be inserted into chromosomes by viruses or mobile elements that can move among the chromosome from cell to cell. 

A mutation is any change in genetic material that results in an alteration of the sequences of bases. Crossing over between homologous chromosomes is not a gene mutation because it occurs during mitosis and meiosis I to shuffle the genetic material on the maternal and paternal chromosomes and does not make any changes to the DNA of the alleles nor do they alter the position of genes on the chromosomes. 

Lecture 3:

What is the difference between the following types of equations:

u*p = v*q vs. u*p = s*q^2

1st one:

p-f(A allele)

q-f(a allele)

u- the forward mutation rate

v- the reverse mutation rate

allele is neutral and S.S. assumed leads to q = u/(u+v)

2nd one:

assume that there is a selective disadvantage s to the a allele and if the a allele is rare, its harmful effect is recessive, the back mutation can be neglected, and at S.S., the 2nd  equation results.

assume p~1, q = (u/s)^(1/2) at appreciable equilibrium, the frequency of the mutant allele can be surprisingly high

With the help of selection and genetic drift, you can increase the numbers of new mutant alleles and cause substantial alterations in allele frequency. 

Lecture 3:

What did  replica plating show?

Lecture 3: 

What is the difference between somatic and germ-line mutations? Mutations and fixations?

Germ-line mutations are mutations that occur in cells that will give rise to gametes, which gives them a chance to be passed on to the next generation.

Somatic mutations occur in other cells of the body and do not give rise to gametes. They can give rise to cancers, antibodies to help fight off infections, are the result of molecular mechanisms and provide no evolutionary consequences. Antibodies are generated as a result of gene arrangement and somatic point mutation. 

Fixations: a tiny minority of mutations that spread through population to become fixed, meaning that there is a substitution of the new allele for the old allele or alleles at the locus. The overwhelming majority of new mutations are lost and have no effect on evolutionary change while very few will become polymorphic and in turn, the fraction of these alleles will become fixed. 

Lecture 3:

What is the result of a population obeying H-W Equilibrium? What did H-W do for Darwin?

no change in allelic nor genotypic frequencies in subsequent generations.

Darwin believed that genetic variation was lost rapidly through blending inheritance, and that natural selection had to start from scratch each generation with whatever variation happened to be induced by the inheritance of acquired characters. 

H-W law showed that genetic variation doesn't disappear in a few generations and can have a long genetic history. Because the allelic frequencies are preserved from one generation to the next, this opens up the possibility that they can be altered over a span of generations. New genetic variability can be built up even though new alleles are introduced by mutation at a slow rate. This opens up opportunities for evolutionary change that Darwin couldn't have anticipated. 

Lecture 3:

List the 5 null assumptions of H-W:

1. mating is random

2. populaton is large

3. no mutation

4. no selection

5. no gene flow

Lecture 4:

What are random assortment and genetic recombination?

Lecture 4:

What are the three patterns of selection that can alter the distribution of phenotypes in populations?

Lecture 4:

Describe directional selection.

The most important type of selection in evolution because it produces allele frequency shifts and phenotypic changes. When organisms at one end of the distribution/bell curve have a higher fitness than those on the other, the phenotypic mean in the next generation will be shifted. 

-usually don't obey hardy weinberg law unless selection is severely weak

Lecture 4:

What did the Grants and their colleagues do with the BMP4 gene? Results?

Lecture 4:

Describe stabilizing selection:

In stabilizing selection, extremes are selected against so that organisms in the middle of the distribution tend to have the highest level of fitness. It keeps phenotypic changes from taking place and it tends to select against changes in allele frequencies 

What can we predict about the fate of genetic variability under

stabilizing selection? Many predictions are possible. If the environment were

to remain constant and stabilizing selection were to continue for a long time, it

might be expected that alleles that do not contribute to the most favored

phenotype would be lost. Individuals with genotypes that tend to result in a

7.5 pound birth weight would come to predominate in the population.

Eventually, a single genotype with the greatest likelihood of giving rise to this

intermediate birth-weight phenotype would be the only genotype that

remains.

Lecture 4:

Describe disruptive selection

Lecture 4:

Describe the two types of chance events that contribute to random genetic drift. 

Other causes of random drift. 

While founder effects can alter allele frequencies in small populations that have become separated from larger populations, size bottlenecks can result in altered allele frequencies. They both are involved in population fragmentation, which involves the subdivision of a randomly mating population so that random mating across the subdivision boundaries is no longer possible. This will lead to accumulation of differences in allele frequencies, speciation, and an acceleration of the rate of loss of genetic variation through random drift, and local/global extinctions.

Differences between the effective population size and the actual size of the population (usually effective size is smaller) can increase the influence of random drift. The balance between introduction of new neutral mutations and their loss through random drift determines how much genetic variability is present in the population.  

Lecture 4:

How can we quantify population subdivision and non-random mating?

What is the difference between identity by descent and state?

The inbreeding coefficient F will measure the probability that at a given locus an individual has two copies of an allele that are identical by descent 

Identity by descent- two alleles that the individual carries had a common ancestor so recently that the copies of the ancestral gene have come down unchanged through the intervening generations

Identity by state- 2 different alleles happen by chance to have converged by separate pathways of mutational change so that they are now identical. They have not come down unchanged by a common ancestor. 

Lecture 5:

What is inbreeding depression?

It involves the harmful effects of inbreeding on fitness, which results from homozygosity for recessive alleles that would be concealed as heterozygotes.

Examples include marriages between close relatives and zoo populations. . For gazella cuvieri, there is a strong negative correlation between inbreeding coefficient and % normal spermatozoa. 

Lecture 5:

Why is population size important?

Lecture 5:

What is Ne?

the females of the swallow-tail butterfly Papilioo dardanus employ batesian mimcry of a distasteful butterfly and moth species from Africa as a defensive mechanism to avoid being a part of a predator-prey relationship with birds, which contributes to genetic polymorphorisms in gene pools for alleles that control wing color and pattern. 

The mechanism behind all of this is gene regulation. The H gene is a highly sophisticated regulatory gene in Papilio females, which behaves as a master regulator of switching on/off entire groups of genes that control different developmental pathways. The frequency of the different alleles of H have been shaped by predation

Gene flow is the flow of genes between gene pools throughn immigration or through the exchange of gametes between gene pools. 

Transient polymorphisms: if strongly advantageous alleles are not lost by random drift during the first few generations, they will increase rapidly in frequency. If the advantageous allele is in the process of replacing the old one, locus will be polymorphic. The polymorphism will disappear as soon as new allele becomes fixed.

Balanced polymorphism- results because balancing selection will maintain genetic polymorphisms for longer periods (maintained by a balance of selective pressures). They play an important role in evolution because genetic variability that has become stored as balanced polymorphism enables populations to change quickly of environmental changes. 

Lecture 5:

Describe the evidence behind mutation-selection balance and heterozygote advantage.

1. mutations are introduced into a population and removed by selection, reaching a frequency at which these rates balance eachother. at equilibrium for harmful recessive allele, q = sqroot(u/s)

2. mutant alleles for sickle cell anemia presist because heterozygotes, which are more resistant to malaria, have higher fitness than the mutant homozygotes or non-sickle cell anemia homozygote allele. Other examples are cystic fibrosis and transgenic mice heterozygotes for common CF allele are more resistant to thyroid infections in their intestines. 

Lecture 6: 

What are the differences between temporal and spatial heterogeneity?

Spatial heterogeneity occurs if the environment is different in different parts of the geographic range of the species; there are 4 subenvironments clustered together and permits the survival of organisms with different genotypes in different parts of the environment. The differential survival is accompanied with reductions in gene flow between all 4 subenvironments to obrain balanced polymorphism in the absence of heterozygote advantage. 

-Example: LDH. If the expression of the LDH gene goes up with high aerobic activity of the fish, this will cause lactic acid, anaerobic breaksown of sugar product from glycolysis, to buildup and cause muscle fatigue. Before this can happen, lactic acid is converted to pyruvic acid with LDH so if PA goes up, there is more available for the aerobic metabolic pathway. LDH frequencies (of a allele) vary with latitude and mean water temperature (such smooth variation between extremes is termed a cline). North-south cline formed as a result of the varying efficiencies of the allozymes at different temperatures. 

The fact that both a and b alleles are found throughout the extensive range of this species means that these two alleles must have existed together for many generations. This polymorphism is maintained by directional selection and restrictions in the free flow of genes. These restrictions allow b alleles to be maintained by directional selection at high frequency in the north at the same time as a alleles are maintained by directional selection at high frequency in the south.

Temporal geneity- more difficult to establish internal equilibrium in a temporally fluctuating environment because there is no opportunity for alleles, once they are lost, to be relenished from other parts of the environment. At only one period only one subenvironment exists so that if an allele is lost during that period through directional selection, it is gone until the mutation reintroduces it. 

-triggers phase polymorphisms (phenotypic polymorphisms that do not relfect underlying genetic variability)

Lecture 6:

What is frequency dependent selection?

Lecture 6:

What is horizontal gene transfer and its role in the evolution of the adaptive immune system?

Horizontal gene transfer is the process by which genes are transferred between species by plasmids, transposons, retrotransposons, and retroviruses. When genes are carried from one organism to another, they can be incorporated into recipient's genome through the enzyme mediated process of recombination. 

This is evident through the rearrangement of the V, D, J, and C antibody gene fragments broken down by the insertion of intervening regions of DNA by the RAG1, RAG2 enzymes. They bind to short recognition sites on stretches of DNA, ligate and loop the DNA together to bring signal regions closer, remove the signals along with intervening DNA. RAG1,2 proteins can be traced back to Transib DNA transposase gene

Lecture 7: 

List the disadvantages of sexual reproduction

1) The breakup of advantageous genotypes.

2) The twofold disadvantage to sex. This disadvantage is traceable to the fact that only

one of the sexes can actually produce offspring, while all the members of asexual species can

produce offspring (Figure below).

3) The susceptibility of sexual organisms to horizontally transmitted sexual diseases.

Lecture 7:

Explain Muller's Ratchet.

Hermann Muller suggested that if all the members of a population carry damaging mutations the average fitness of the population will ratchet down one notch and be unable to recover unless recombination gives rise to undamaged organisms again.

Muller imagined a finite population of asexually reproducing organisms in which

harmful mutations are occurring. Suppose that by a combination of mutation and drift all the members of the population acquire harmful mutations in a given generation. When this happens the fitness of the entire population is lowered — one click of an irreversible ratchet.

There is, however, a way to escape the effects of the ratchet. If some of the organisms in such a population acquire the ability to outcross and piece together undamaged pieces of DNA from more than one individual, they can recreate the original mutation-free genotype in some of their offspring. In other words, sexual reproduction can reverse the ratchet.

During the early evolution of eubacterial cells, when mutation rates were high and

DNA repair was much less efficient than it is today, Muller’s ratchet may have been an

important mechanism that provided an advantage to the ability to transfer and recombine genes. The ratchet is less likely to play a role in the maintenance of sex in most present-day organisms, because they are good at repairing their genetic material and mutation rates may not be high enough to fix harmful genes even when populations pass through severe size bottlenecks.

Lecture 7:

When is sex advantageous?

in a temporally diverse environment

if Pathogens Make the Future Unpredictable — Red Queen Races and Arms Races

Red Queen races are defined as a series of evolutionary responses to continual changes in the physical or biological environment that maintain fitness but that do not result in large changes in gene function.

In evolutionary arms races, in contrast, organisms adapt to a series of large changes in

their predators or pathogens by evolving new types of attack and defense.

Lecture 7:

What is Darwinian fitness? factors?

It is the relative probability that an organism will survive and reproduce, compared with the average for all the members of the population.

factors:

1. survival to reproductive age

2. intraspecific competitive ability for resources (other members of the same species)

3. interspecific competitive ability (other members of a different species)