Describe the plight of the greater prairie chicken in Illinois, what conditions led to this change, and how many birds were still alive in 1994?   

Inbreeding à little gene flow, high genetic drift, nonrandom mating was not well facilitated by small population size

Each generation, banded snakes migrate to islands keeping the banded allele in the population.

How far can allele frequencies change on the island in the “one-island” model? 

Tend toward the same as the mainland allele frequencies. They cannot change more than that.

Is evolution by natural selection random?  Could evolution ever be random and if so how?   

No. Genetic drift is random.

Chose 10 zygotes from figure 7.10 and be prepared to report your allele and genotype frequencies in class.  

5 A1A1, 3 A1A2, 2 A2A2 à 13 A1, 7 A2 à .65 A1, .35 A2

How does increasing the population size of the zygotes affect the cumulative outcome of simulations such as that carried out in question 9?  

It reduces the sampling error of chance events. It prevents genetic drift from directing allele frequencies to fixation and brings frequencies to their equilibrium

New populations from larger populations have different allele frequencies from the previous pop, and are more prone to genetic drift since the pop size is smaller. Silvereyes moved from island to island, and genetic diversity decreased steadily after each colonization event.

A founder pop of 20 people contained one heterozygote for a LOF allele of CNGB3. 4 generations later, the mutant allele began appearing in the pop. (Bottleneck)

1)The frequency of heterozygotes in a pop.

2) Heterozygosity tends to decline over generations

3) Small pop size causes heterozygosity to decline more rapidly than large populations

Initial frequency is related to the probability of fixation. You will see a loss in heterozygosity of 1% every generation due to genetic drift.

Hg+1 = Hg[1-(1/2N)]

What is the formula for calculating the frequency of heterozygotes across any allele frequency of p?  

P^2 + 2pq + Q^2 = 1

Buri’s 107 populations of 8 heterozygous flies underwent 19 generations. At the end, 30 pops lost the bw75 allele (0) and 28 pops went to fixation of bw75 (1). Yes, the theoretical and experimental results supported each other. 

Settlers in Missouri clearcut Ozark woodlands and suppressed fires, then oaks/hickory forest invaded, then eastern red cedars invaded glades.

What was Tempelton’s prediction for the collard lizzards and why did he think this?   

He predicted that since the populations were small and genetically isolated, genetic drift would be significant in populations; most loci would be fixed for a single allele, and genetic variation would be low.

Populations were relocated to empty glades and controlled burns of oak-hickory forest created paths for lizard migration to other glades.

Rate of substitution = mutation rate

What two camps are there in the circle of evolutionary biologists about the frequency at which new mutations go to fixation rapidly because of natural selection.  Describe these two view points.   

Neutral theorists- (Motoo Kimura) hold that advantageous mutations are exceedingly rare and that most alleles of genes are selectively neutral. They predict that for most genes in most pops, the rate of evolution will be equal to the neutral mutation rate.

Selectionist theorists – hold that advantageous mutations are common enough that they cannot be ignored. They predict that for many genes in most populations, the rate of substitution will reflect the action of natural selection on advantageous mutations.

What explains the clock-like evolution of gene or protein sequences? 

What did Kimura predict the rate of evolution would be equal to? 

Rate of molecular evolution = mutation rate

What type of genes are most useful for developing an unbuiased molecular clock?  

Pseudogenes

What is a silent site and a replacement site and which one is likely to mutate faster and why?

Silent site - DNA sequence changes that do not result in amino acid changes.

Replacement site – Sequence changes that do result in amino-acid change

Silent sites mutate faster because they are not exposed to natural selection on protein function.

What type of selection does the answer to question 25 indicate (imply)?

Positive selection (if it shows up). Purifying selection (no change is tolerated)

Why do genes for histone proteins evolve at a very slow rate?

Histone function is vital to cellular processes regarding structural integrity of the nucleosome. There is high selection against deleterious alleles. (Functional constraint)

Combo of pop size and generation time. They are complementary.

Dn is the rate of nonsynonymous substitutions per site and Ds is the rate of synonymous substitutions per site. High Dn/Ds indicates a lot of advantageous replacement mutations (Positive selection).

What is the MHC and the ARS of the MHC.  How did selection vary between the ARS of the MHC and other exons of the MHC gene(s)?

A cluster of genes that display pathogen proteins - Major Histocompatibility Complex. The Antigen Recognition Site is the part of an MHC protein that binds to the foreign peptide. There were more replacement site mutations than silent mutations. Other exons of the MHC genes showed more silent than replacement mutations.

How is exon 11 of the BRACA1 gene evolving and why?  How was this discovered

It is evolving in Humans and chimps by positive selection. It is unknown why, but it relates to breast cancer. It was discovered by a Dn/Ds comparison among mammals. The Dn/Ds was greater than 1 in humans and chimps.

Explain the theory behind the Macdonald-Kreitman test.  

2 fly pops in different environments. Can we detect positive selection? Compare Dn and Ds mutations. Comparing Dn/Ds ratios BETWEEN pops is more accurate detection of positive/negative selection than comparing Dn/Ds rations WITHIN pops.

What % of replacement polymorphisms were fixed in between versus within species comparisons and what is the implication of that? 

29% between. 5% within. There is more divergence between species, and less evolution within the species.

What type of genes are most likely to be undergoing positive selection?

Codon bias – (transcriptional efficiency) some tRNAs (and codons) are more readily available for faster translation. An mutation calling for an unavailable tRNA-even if it has the same amino acid- might not be…

Hitchhiking/Selective Sweeps occurs when strong positive selection acts on a particular amino acid change and neutral or slightly deleterious mutations in nearby loci increase in frequency as well. This happens because recombination fails to break up the linkage between the hitchhiking sites and the site under selection. 

Negative selection against deleterious mutations.

If you saw a region of a chromosome that had remarkably little variation within a diverse species, what molecular process would you use to explain that?

Hitchiking: a highly advantageous mutation would be broken up by recombination, so recombination rate is not as common at that site.

Data for substitutions in all species. Have to know whether a mutation is beneficial or deleterious.

Supported- It’s a theory, but overstated

Decreases hetrozygosity

How does inbreeding affect gene frequencies in the next generation?

Allele frequencies do not change.

F- probablilty that both alleles in an individual are identical by descent

What is inbreeding depression and how would you define it algebraically?

Exposure of deleterious recessive alleles to selection.

Describe the magnitude of inbreeding depression in humans

High.

What is mutational meltdown and explain this using the prairie chicken example.  

Probablilty of exposure to deleterious mutation increases when pop size is small.

When a mutation, pop size, and genetic drift interact in a downward trend