NS2750 Prelim2 2016 Answer Key

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ Section 1 (max = 30) ________________ ________________ Section 3 (max = 40) ________________ Section #1 (30 points) _______________ Section #2 (20 points) _______________ Section #3 (30 points) _______________ Section #4 (20 points) _______________ Total (Max = 100) _______________  Print your name in LARGE letters on the BACK OF THE LAST PAGE of the exam.  Your TA (please circle one) Yiping Wang Yiqin Wang Cem Atillasoy Nicole Calautti Shuo Chen Megan Fitzgerald Deborah Modlin  Print your name in LARGE letters on the BACK OF THE LAST PAGE of the exam.  There are four sections to this exam:  Section 1: Multiple Choice questions. You should answer 10 of the 11 questions. Each question is worth 3 points, for a maximum total of 30 points. If you answer a question but then decide you don't want it graded, put an X through your answer. The same for the other sections.  Section 2: True/False questions . You should answer 10 of the 11 questions. Each question is worth 2 points, for a maximum total of 20 points.  Section 3: Short Answer Questions I . You should answer 5 of the 6 questions. Each question is worth 6 points, for a total maximum of 30 points.  Section 4: Short Answer Questions II . You should answer BOTH questions. Each question is worth 10 points, for a total maximum of 20 points. Each student in this course is expected to abide by the Cornell University Code 1

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ SECTION 1: MULTIPLE CHOICE QUESTIONS (30 points)  Answer any 10 of the following 11 multiple choice questions. If you answer more, only the first 10 will be graded. (3 points each for 30 points). There is only one correct answer for each question. 1. Which of the following types of transposable elements does not go through an intermediate RNA phase during transposition? A. LINEs B. SINEs C. DNA transposons (Correct) D. Retroviruses and retrovirus-like LTR 2. Which of the following populations has the lowest levels of linkage disequilibrium? A. Africans (Correct) B. Asians C. Europeans D. Native Americans 3. Which of the following dog populations went through more population bottlenecks? A. Village dogs B. Purebred dogs (Correct) C. All dog populations went through the same number of bottlenecks. D. Wolves 4. Which of the following is a limitation of GWAS? A. Many disease-associated genetic variants are not causal B. There is a large environmental impact that GWAS does not address C. GWAS focuses on common variations D. All of the above (Correct) 5. Which population has the highest level of genetic variation? A. Africans (Correct) B. Asians C. Europeans D. Native Americans 6. Which of the following are true about complex disorders? A. Multiple genetic and environmental causes B. Aggregate in families C. Do not segregate as described by Mendelian genetics D. All of the above (Correct)

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ SECTION 2: TRUE/FALSE QUESTIONS (2 points each for 20 points)  Answer any 10 of the following 11 TRUE/FALSE questions. If you answer more, only the first 10 will be graded.  Mark T for TRUE of F for FALSE in the space provided. 1. Denisovans are considered a separate population from both Neanderthals and modern humans. T 2. Asians currently have the largest effective population size in the world. F 3. According to the near-neutral theory of evolution, no deleterious mutation can ever rise to high frequency within a population. F 4. The cost of genome sequencing obeyed Moore's Law. F 5. Humans are one of the most genetically diverse species ever studied. F 6. Transposable Elements were discovered by Barbra McClintock. T 7. The most common type of transposable element in humans are LINEs. T 8. In Adam Boyko’s lecture on canine genomics, he hypothesized that dogs evolved in Central Asia. T 9. Agricultural revolution led to significant population increasing. T 10. Alcohol flush reaction is caused by the accumulation of alcohol in the blood stream. F 11. The interbreeding of Neanderthals and our ancestors outside of Africa resulted in an introgression of Neanderthal-derived DNA in modern non-African human population. T

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ SECTION 3: SHORT ANSWER QUESTIONS I: (6 points each for 30 points)  Answer 5 of the following 6 questions. If you answer more, only the first 5 will be graded. Limit your answers to the space provided below the question. 1. What is the major difference between the neutral and near-neutral theories of evolution, concerning slightly beneficial or deleterious alleles? Which theory predicts a higher prevalence of genetic drift (i. e. a higher percentage of genes whose evolution is determined by drift)? Near-neutral theory focuses on the evolution of slightly deleterious or advantageous mutations (1), and predicts that it is controlled by genetic drift instead of selection. (1) Slightly advantageous mutations (0.5) may not necessarily rise to high frequency (0.5), but instead die out (1). Similarly, slightly deleterious mutations (0.5) may not necessarily die out (0.5), but instead rise to high frequency (1). 2. What are the two enzymes that are involved in the pathway for breaking down alcohol in humans? How does a deficiency in this pathway cause alcohol flush syndrome? In which population is alcohol flush syndrome most common? Alcohol dehydrogenase breaks down ethanol to acetaldehyde, acetaldehyde dehydrogenase breaks down acetaldehyde to acetic acid. (2) Mutations that upregulate alcohol dehydrogenase and downregulate acetaldehyde dehydrogenase cause buildup of acetaldehyde (1), leading to alcohol flush syndrome. (1) These mutations are most common in Asian populations (2), where they protect against alcohol poisoning due to rice wine. 3. How does genotype-based personalized nutrition differ from population nutrition? Genotype-based nutrition takes into account genetic variations that change the amount of nutrients each person requires and their response to those nutrients, so diets are personalized to each person (3). Population-based nutrition is an average approach whose nutrition recommendations are designed to work most people in a population (3).

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ SECTION 4: SHORT ANSWER QUESTIONS II (10 points each for 20 points)  Answer BOTH questions. To conserve space and time, do not repeat the question in your answer. Limit your answers to the space provided below the question. 1. What is GWAS (1 point)? Why is GWAS better than the traditional way of genetic mapping for disease genes (2 points)? Briefly describe the theoretical basis (3 points) and experimental steps (4 points) for this approach to identifying disease-associated mutations. GWAS is a genome-wide association study (0.5), and links genetic variation to its effects on disease risk (1.5). It is better than pedigree analysis because disease-causing SNPs can be localized more precisely (1), due to the fact that more recombination takes place in an unrelated GWAS sample, leading to smaller LD blocks (1). GWAS can also detect more SNPs with small effect on disease risk (1), because of greater statistical power from larger sample size (1). Steps: Select a group of samples to sequence (0.5), both patients and controls (0.5). Sequence or genotype samples (1). Run statistical tests to associate SNPs in samples to disease risk (1) Cluster significantly associated SNPs (1)

NS/ANTH 2750: Human Biology & Evolution Prelim Exam #2, 11/4 10:10 – 11:00 am Name:___________________________ 2. We discussed two methods in class that can be used to detect adaptive evolution: dN/dS and haplotype length. 1) Please describe these two methods (2 points each) and also explain the theoretical basis for either method (3 points each). dN/dS is ratio of nonsynonymous to synonymous (1), < 1 indicates negative selection, ==1 indicates neutrality, > 1 indicates positive selection (1) This is because nonsynonymous mutations cause an amino acid change, while synonymous mutations do not (3) Long haplotypes (1) indicate positive selection (1). This is because recombination breaks up haplotypes (2), and positive selection takes less time than genetic drift, leading to longer haplotypes on average (1).