1. Briefly define and state the significance of the following terms (4 points each; ·= 20)

eidos

Germline sequestration

Fundamental theorem of natural selection

Genetic hitchhiking

Inbreeding Coefficient

2. Clearly state the important distinction between (7 points each; ·= 34):

Locus / Allele

Adaptation / effect

Some formulas: random variance in p = pq/2N p2 + 2pq + q2 = 1

pt+1 = pequil = pt+1= pt(1-u)+qt(v)

f(A) at equilibrium = pequil = with WAA = (1-s), Waa = (1-t) L =( Wopt - Wbar)/Wopt

= _Ne = ppop1 t+1 = ppopl t (1-m) + ppop2 t (m) F=(He - Ho)/He

2. Why was the variation observed among domesticated animals so important to Darwin in advancing his theory of evolution by natural selection? (6 points; ·= 40)

3. In a population of haploid bacteria with an effective size of Ne = 1000, half the bacteria (500) carry a wild type allele that has a fitness of 1.0 and the other half (500) carry a mutant allele that has a fitness of 0.99. You are asked to change the population size of this bacterial culture so that the two alleles have the same realized fitness. Should you increase or decrease the effective population size? At what effective population size would these two alleles have the same realized fitnesses? (4 + 2 = 6 points; ·= 46).

4. The Eugenics movement was active in the early decades of this century and sought to improve the genetic characteristics of the human population by preventing individuals with various undesirable traits from reproducing. Recognizing that most deleterious traits are recessive, use your knowledge of population genetics theory to argue a strong case against the effectiveness of such programs in eliminating these mutations from the human population. (8 points; ·= 54).

5. For a single locus with two alleles, give relative fitness values of the genotypes which would result in: A) directional selection, B) stabilizing selection, C) disruptive selection. Clearly identify which fitness values are assigned to each genotype in all three cases. (12 points; ·= 66)

6. Genetic load is a general concept but there are a number of different ways in which this can be illustrated in population genetics (in lecture we discussed two examples: segregational load and substitutional load). An additional example is recombinational load. Briefly describe what is meant by this term and how recombination may be related to genetic load. (8 points; ·= 74)

7. Ross Perot was elected president and he decided to eliminate the national debt by cultivating and marketing marijuana. In an effort to realize the best return on his investment, Ross began research into the yield of three different species of Cannabis, and obtained the data below: 1) the variance in yield among individuals within highly inbred strains of each species that were grown at Ross's farm in Texas, and 2) the variance in yield among individuals within natural wild populations. From these data i) estimate VG and write your estimate in the table below (recall VP = VG + VE). From these data, what would be ii) the best species to develop as cash crop, iii) the worst species to develop as a crop, iv) Clearly show and state why. (14 points; ·= 88)

8. In a recent study of the evolution of the ND5 protein coding gene in mitochondrial DNA in some closely related species of fruit flies, it was observed that the rate of DNA evolution was greater along the lineage leading to Drosophila melanogaster than along the lineage leading to D. simulans (see figure; branch length indicates approximate relative rate of DNA evolution for all nucleotide sites). In an effort to understand the cause of this pattern, the data were broken down into the number of silent (synonymous) and replacement (non-synonymous) nucleotide differences between pairs of the three species. These data are shown in the table. In class we discussed two general aspects of DNA evolution that can affect the rate of DNA divergence between species. From these data i) identify which of these two biological processes best accounts for the faster rate of evolution in D. melanogaster, and ii) clearly explain your choice (you can assume the data have been corrected for multiple changes at the same site). (12 points ·= 100)

# of Silent Differences # of Replacement Differences

D. mel. vs. D. sim. 53 17

D. mel. vs. D. yak. 103 46

D. sim. vs. D. yak 88 44

9. You are a conservation biologist attempting to save the endangered Northern Spotted Owl in a captive breeding program but have the financial resources to collect owls from only one population this summer. The census data below indicate the number of breeding individuals in each of two populations over the past four summers (assume for simplicity a one year generation time and that these breeding individuals represent the entire population). From which population would you collect? Justify your answer quantitatively and qualitatively. (16 points)

Population sex 1990 1991 1992 1993

1 F 20 20 10 40

M 20 20 10 40

2 F 40 40 10 40

M 40 40 2 40

______________________________________________________________________________

Some formulas:

pt+1 = pequil = pequil = pt+1= pt(1-u)+qt(v)

Random variance in p = p q/2Ne

= ·Ne = ppop1 t+1 = ppopl t (1-m) + ppop2 t (m)

uniformitarionism

Requirements for Natural selection

polymorphism

cline

homology/analogy

grade/clade

paraphyletic

character polarity

what's worse a data set full of honmplasious characters or one full of autaopmorphous characters

compatability

build a upgma tree and test for relative rate differences

something with molecular systematics

superposition

angular uncomformity

index fossils

contigency

wallace's line

mesosaurus

provicialized

congruence

dominance/additive model

some problem illustrating the effect of dominance/additivity on genetic variation

given axes draw curve of overdominance

germline sequestration

what is the recombination rate for loci on two separate chromosomes

how could a mutation that doesnt affect phenotype play a role in the origin of species?

800 AA 1200 Aa 500 aa Are these in H-W equilibrium? what are p and q after random mating

2800 A's 2200 a's; p=.56

Drift and the variance within vs. between

Pop. of 5000 goes from p=.5 to p=.4 in one generation due to drift, mutation or selection

population losing size: bottlenecks vs loss of one sex which is more crucial: do calculations

mutation drift balance

differentiation in an island-continent vs stepping stone model with calculations of gene flow

selection against heterozygotes

selection gene flow balance in two environments with different relative fitnesses

rate of change proportional to genetic variance in population

linkage vs. linkage disequilibrium

effect of recombination on rate of decay of linkage disequilibrium

selection of and selection for

select differentially for two linked loci (without/with recombination)

selection on two loci with epistasis

describe forces that might prevent the evolution of populations by shifting balance

adaptive landscape