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NAME_______________________________ EXAM#_______ 1 1. (15 points) Next to each unnumbered item in the left column place the number from the right column/bottom that best corresponds: 1) a Darwinian theory of phenotypic evolution influenced by Lyell's 20 abnormal 4:4 segregation principles of geology 2) a geographically widespread population subdivided into local demes 21 colchicine among which migrant individuals are exchanged 3) a molecular evolutionary phenomenon that illustrates traditional 8 constitutive heterochromatin Darwinian natural selection 4) a species concept that pertains only to sexually reproducing lineages 27 fundamental niche 5) a specific endogenous retrovirus in humans 6) common in a population whose inbreeding effective size is very small 1 gradualism 7) condensed in interphase in only some cells 8) contains highly repeated DNA sequences 15 HIV 9) Darwin's theory of the spatial dimension in multiplication of species 10) factors that prevent members of a sexually reproducing species from 6 identity by descent recognizing members of another species as appropriate mates 11) factors that disrupt the development of zygotes formed by fusion of 24 Mendel's Second Law gametes drawn from two different species 12) four chromatids to same pole in meiosis I 2 metapopulation 13) illustrated by replacement of hemoglobin ß alleles A and S by allele C in some western African populations 25 phylogenetic species concept 14) inhibits chromosome movement by binding to centromeres 15) Its envelope protein evolves by natural selection during the infection 19 polytene chromosomes of a host. 16) Law of Segregation 10 prezygotic barriers 17) most frequent in populations that have high heterozygosity 18) occurs when the average excesses for fitness of all alleles at a 18 selective equilibrium polymorphic locus equal zero but broad-sense heritability is nonzero 19) permit construction of haplotype trees for chromosomes 3 of Drosophila 22 selfish DNA elements persimilis and D. pseudoobscura 20) postmeiotic segregations present 29 Turner's syndrome 21) prevents formation of spindle 22) retrotransposons and retroviruses are examples 23) reveal extensive translocation polymorphism in Drosophila pseudoobscura. 24) segregation of each gene pair independent of all others 25) taxonomically recognizes all diagnosably distinct evolutionary lineages 26) the actual resources used by a species at a given time and place NAME_______________________________ EXAM#_______ 27) the set of environments/resources that a species is capable of using 28) violates assumptions of the two-dimensional stepping-stone model of population structure 29) XO 30) XXY 2 NAME_______________________________ EXAM#_______ 2. (4 points) You are given two pure-breeding strains of snapdragon. One has white flowers and the other has red flowers. When plants from the two strains are intercrossed, the F1 plants are all red flowered. When these F1 plants are crossed to plants from the pure-breeding white strain, 3/4 of the progeny are white flowered and 1/4 are red flowered. Explain these results using gene symbols of your own choice. 3 NAME_______________________________ EXAM#_______ 3) (10 points) Draw the appearance of a pair of telocentric homologs and state in words the main chromosomal event(s) that occur in each of the stages of meiosis I listed below. Be sure to indicate when the following events occur: synapsis, crossing over, and loss of sister chromatid adhesion. In your drawings, assume a single crossover occurs between the two homologs, and distinguish sister chromatids from the two homologs by using different colors or by using smooth and wiggly lines. zygotene pachytene diplotene metaphase I anaphase I 4 NAME_______________________________ EXAM#_______ 4) (5 points) In corn, the genes for tassel length (alleles T and t) and pale leaves (alleles P and p) are known to be on different (nonhomologous) chromosomes. In the course of making routine crosses, a geneticist noticed that one T/t; P/p plant gave unusual results in a testcross with the double recessive homozygote t/t; p/p. The results were: Progeny: T/t; P/p t/t; p/p T/t; p/p t/t; P/p 1032 1016 14 16 a. Draw the appearance of the chromosome(s) carrying these genes at pachytene in the unusual T/t; P/p plant. Indicate positions of the T, t, P, and p alleles in your drawing. b. Explain very briefly the origin of the classes of progeny having 14 and 16 members. 5 NAME_______________________________ EXAM#_______ 6 5) (15 points) Identify each of the following equations and its relevance to population genetics, including an explanation of all parameters. Indicate as appropriate any assumptions made by these expressions regarding the number of alleles present at any locus or variable site being studied. (3 points each) a. p' = p2 + 1/2(2pq) The expected frequency of an allele following one generation of random mating (p') equals the initial frequency of homozygous genotypes for that allele in the population (p2) plus half the frequency of heterozygous genotypes (2pq; assumes that only two alleles are present in the population). b. D’ = D/Dmax where D = gABgab - gAbgaB and Dmax = lower value of p1 q2 or p2 q1 D’ is a standardized measure of linkage disequilibrium between two loci or variable SNP sites that varies from 0 (no disequilibrium) to 1 (maximum disequilibrium). D is an unstandardized measure of linkage disequilibrium. p1 = frequency of allele A at the first site/locus, p2 = frequency of allele a at the first site/locus, q1 = frequency of allele B at the second site/locus, q2 = frequency of allele b at the second site/locus. g terms are the gametic frequencies of haplotypes AB, ab, Ab and aB as indicated by the subscript. Dmax is the maximum level of disequilibrium possible for the population with the given allelic frequencies. The equation assumes two allelic forms at each locus/site in the population. c. Rate of Evolution =Rate of Input X Rate of Loss = (2N)µ1/2N = µ T long-term of neutral evolution of a locus or protein. Rate of input of neutral mutations is twice the inbreeding effective size (N) of the population times the neutral mutation rate per locus. The rate of loss of alleles is 1/ 2N. The N terms cancel, so the long-term rate of neutral evolution equals the rate of mutation to neutral alleles. d. dn = do(1-2m)n ifference in frequency of an allele between two populations at generation n (dn) equals the difference in frequency at generation 1 (do) times 1 minus 2m to the nth power, where m is the portion of each population that migrates to the other one each generation. The expression assumes that m is symmetrical and constant across generations. e. FST = (HT - HS)/HT FST is the standardized variance in allelic diversity (varies from 0 to 1) between two or more demes (= subpopulations) of a population. Heterozygosity for the total population (HT) equals 1 minus the sum of squared allelic frequencies measured for the population as a whole. Heterozygosity for NAME_______________________________ EXAM#_______ 7 subpopulations is the average of 1 minus the sum of squared allelic frequencies calculated for each subpopulation separately. FST measures the interaction between gene flow between subpopulations (lowers FST) and genetic drift within subpopulations (raises FST). (Heterozygosities may be calculated also as the sum of all heterozygote [2pq] terms for all pairs of alleles in a population.) NAME_______________________________ EXAM#_______ 8 6) (15 points) Identify each of the following equations and its relevance to quantitative genetics, including an explanation of all parameters. Indicate as appropriate any assumptions made by these expressions regarding the number of loci or alleles present at any locus being studied. (3 points each) a. s2 = [(x1- µ)2 + (x2-µ)2 + … + (xn- µ)2]/n The variance (s2) of a phenotypic trait in a population is calculated as the average squared deviation of each individual phenotype (x1, x2 . . . xn) from the population mean (µ), where n = number of individuals in the population. b. σ2p = σ2a + σ2d + σ2i + σ2e Fisher's analysis of phenotypic variance (σ 2p) into components including additive genetic variance (σ 2a), dominance genetic variance (σ 2d), epistatic genetic variance (σ 2i) and environmental variance (σ 2e, the variance not explained by the modeled genetic variation). At least two loci must be considered to have epistatic variance. c. Corr(Sib1,Sib2) = 1/2h2 +1/4σd2/σp2 The measured correlation coefficient between siblings for a phenotype (left term of equation) equals half the narrow-sense heritability (h2 , ratio of additive genetic variance to total phenotypic variance) plus one quarter of the ratio of the dominance genetic variance (σ d2) to the total phenotypic variance (σ p2). (Results may be compared to correlation coefficient between parents and offspring to partition genetic variance into additive and dominance components.) d. aA = p(WAA-W) + q(WAa-W) The average excess for fitness of allele A in a population (aA) equals the probability that a gamete carrying A will be fertilized by another A gamete (p) times the genotypic deviation for fitness of the resulting genotype (AA) plus the probability of fertilization by an a gamete (q) times the genotypic deviation of the resulting Aa genotype. WAA = average fitness of AA genotype; WAa = average fitness of Aa genotype; W = average fitness of the population. The expression assumes two alleles (A and a) at the locus being studied. . Δp = paA/W NAME_______________________________ EXAM#_______ The expected change of frequency of allele A caused by selection (Δp) following a generation in which the initial frequency of A is p, the average excess for fitness of A is aA, and the average fitness of the population is W. 9 NAME_______________________________ EXAM#_______ 10 7) (12 points) The accompanying figure is a haplotype tree constructed from sequences of homologous protein-coding genes from 10 primate species. Branches on the tree are designated by letters (A-R). Numbers on the branches are the inferred dN/dS values. a. (4 points) Identify and describe the methodological principle used to construct a haplotype tree (as shown) from haplotype data and to identify the substitutions occurring on each branch. Parsimony - Find the tree that requires the smallest total number of substitutions to explain the observed haplotypic variation. b. (2 points) Define the terms dN and dS. dN - the number of nonsynonymous substitutions per nonsynonymous site inferred for a branch dS - the number of synonymous substitutions per synonymous site inferred for a branch (A nonsynonymous base substitution causes an amino acid substitution in the encoded protein; a synonymous substitution does not cause an amino acid substitution in the encoded protein.) c. (2 points) Considering the tree as a whole, what is the most prevalent consequence of natural selection with respect to evolution of the encoded protein? What data support this conclusion? Selection mainly acts to conserve the amino-acid sequence of the protein because most branches have a higher rate of synonymous than nonsynonymous substitution (dN/dS < 1). d. (2 points) Which branches contain the strongest evidence for selectively-driven amino-acid substitutions in the protein? NAME_______________________________ EXAM#_______ 11 H and M e. (2 points) Which single branch would be the main focus of attention for someone looking for mutations whose reversal is likely to be associated with genetic disease in humans? Why? H, because selectively-driven amino-acid substitutions are indicated for this branch (dN/dS > 1), and it is ancestral to humans. NAME_______________________________ EXAM#_______ 12 8) (8 points) Match the organism in the first column with the concept that was illustrated in lab using that organism (in the second column). Choose all concepts that apply to each organism (some may have more than one answer). ____H____ onion ____A____ corn pollen ___E, F____ Drosophila ___I, C____ Brassica rapa ___C, D___ humans A. Mendel’s first law B. Mendel’s second law C. polygenic traits D. Hardy-Weinberg equilibrium E. chromosomal aberration F. sex linkage G. meiosis H. mitosis I. artificial selection J. gene flow 9) (4 points) In the HIV computer lab, we were testing the hypothesis that the presence of an SI mutation in more than half of the HIV sequences present in an HIV+ patient is associated with a severely compromised immune system. a. What data from your chosen subject did you examine to test the hypothesis? We looked at the HIV sequences present from the last visit of a given patient. b. What did the ClustalW program do? Describe how using ClustalW was important for testing the hypothesis. ClustalW aligned all of the HIV sequences, so it was easy to find the amino acid residue present at the site of interest (usually position 306) for determining whether or not the SI mutation was present. 10) (2 points) In general, did the FST values you calculated in the gene flow experiment with T. saxatilis indicate that there was a lot of gene flow among the grasshopper subpopulations, or very little gene flow? a lot of gene flow NAME_______________________________ EXAM#_______ 13 11) (10 points) Identify by name the concept corresponding to each of the following statements. (2 points each) a. An evolutionary lineage that maintains its cohesiveness over time because it is a reproductive community capable of exchanging gametes and/or an ecological community sharing a derived adaptation or adaptations needed for reproduction. cohesion species concept or Templeton's species concept b. “. . . all our plants and animals have descended from some one form into which life was first breathed.” common descent (Darwin's theory of common descent or Darwin's theory of descent with modification) c. Past geological events can be explained using laws of physics and chemistry that have remained constant since the origin of the earth. uniformitarianism d. Formation of a new species by hybridizing two different species followed by endoreduplication giving complete copies of the diploid genomes of each parent species in the genome of the new species. allotetraploidy or allopolyploidy e. The synthesis of Darwinism and the chromosomal theory of inheritance. neo-Darwinism