Evolutionary Biology Problem set 1

Biology 32: Evolutionary Biology Problem set 1, 2010 Please write legibly, show all work, & indicate unambiguously the answer to the question (or sub-question). Due date: my office (LSB 224), 5pm, Friday,12 February. 1. The following DNA sequence represents the beginning of the coding region of the alcohol dehydrogenase (Adh) gene, arranged into codons. CCC ACG ACA GAT CAG ACC TTA TCC AGG TGC GAA CTA TGT (a) What is the corresponding mRNA sequence? …the amino acid sequence? (b) Determine for each site in codons 1, 4, 9, & 12 how many possible point mutations are synonymous or non-synonymous. For these four codons collectively, what proportion of the possible mutations at first, second, and third base positions are synonymous? (c) Using the same codons as above, collect data to assess whether the proportion of synonymous mutations differs between transitions and transversions. Specifically, what proportion of transitions (or transversions) result in synonymous substitutions? (d) What would be the effect of an insertion of a single nucleotide "C" between sites 24 and 25 in the nucleotide sequence? 2. Below are gels showing the banding patterns for four different allozyme loci (labeled 1-4 below) in 11 individuals (lanes A–K, from left to right). For each locus, identify the individual genotypes and determine the number and frequency of alleles for that locus. Also, determine the percentage of polymorphic loci in this sample and calculate average heterozygosity among individuals. 3. Two populations, one five times as large as the other, differ in the frequencies of alleles (A versus a) at a certain autosomal genetic locus. The frequency of A in population 1 is 0.60 and the frequency of that allele in the larger population (population 2) is 0.40. Determine the expected allele and genotype frequencies if the two populations are merged and random mating takes place. 4. Assume that the probability of a child being a boy is 0.52. What is the probability that a family would have three consecutive girls? What is the probability that a family would have two boys and a girl? 5. A population of 798 woodchucks is in Hardy-Weinberg equilibrium with respect to a locus coding for coat color, at which there are two alternate alleles, B1 and B2. Black coats are dominant to brown coats (B1B1). Careful observation reveals that there are 112 individuals with brown coats. (a) What are the allele frequencies in the population? (b) What are the genotype frequencies at this locus? (c) How many individuals are heterozygous for this locus and what is their coat color? 6. Imagine a population in which there are four alleles of a short gene. Using the following alignment and the given frequencies of each sequence in the population, calculate nucleotide diversity in this population. Express in words the meaning of this result. Allele 1 2 3 4 ATCGTTCAGG--TCTTGGACATTAAGACAAAAAACATGCATAGCAT ATG-ACAGGGGGTCATGGACAATAAGTCAA----CATCCACAGAAT ATA-ACAGGCGGTCATGCACAATAAGTCTA----CATCGACAGAAT ATG-ACAGGGGCTCTTGGGCAATTAGTCAG----GATCCACAGAAT Frequency 0.40 0.08 0.02 0.50 7. The inability to taste PTC (phenylthiocarbamide) is due to an autosomal recessive gene in humans. If 57% of the people in a population can taste PTC and the population is at Hardy-Weinberg equilibrium with respect to this locus... (a) What are the allele and genotype frequencies in the population? (b) If two parents are tasters, what is the probability that their 3 children will be tasters? 8. Shell color in the European snail is controlled by three alleles at a single locus: CB (brown), CP (pink), CY (yellow). The brown allele is dominant to both pink and yellow; pink is dominant to yellow; yellow is completely recessive. In one population of snails, there are 472 brown snails, 462 pink snails, and 66 yellow snails. Assuming Hardy-Weinberg equilibrium, what are the allele frequencies? 9. At the PGI locus in the Ojibway Pond population of Daphnia, Spitze (1993) found two alleles, S and S-, and the number of individuals with each genotype was 42 SS, 48 SS-, and 38 S-S-. Test these data for deviations from HWE. You will need to calculate (a) expected frequencies and (b) numbers of the different genotypes, and (c) use a chi-square test to determine if there is a departure from HWE. If so, what is the nature of the deviation (e.g., too many SS homozygotes, etc.)? See * below. 10. In his study of Lobelia spicata, Stanton-Geddes used electrophoresis to study the gene coding for phosphoglucose isomerase (Pgi) in the Fort River population in Amherst. He found the following numbers of each genotype: A1A1=52, A1A2=18, and A2A2=5. Test his data for deviations from HWE by first calculating the (a) expected frequencies and (b) numbers of the different genotypes, and then (c) using a chi-square test to determine if there is a departure from HWE. If so, what is the nature of the deviation? See * below. * For questions 9 and 10, use the simplified chi-square table (Table E) to determine if there is a significant departure from HWE. Remember to report the test statistic, the appropriate degrees of freedom (df), the critical value (from the table), and associated probability.