06 Aug Assignment 2, BIOL4390, Population Genetics, Prof.
Assignment 2, BIOL4390, Population Genetics, Prof. A. ZayedFeb 2020Assignment 2 [ 20 % ]Due during lecture, Feb 24 2020 [late submissions will not be accepted]Write Dataset #s on first/title page of your assignment [-1 mark for not doing this!]This assignment will involve analysis of 6 populations of the charismatic and mystical scarabbeetle Khepri amrozayedi, genotyped at 6 microsatellite loci. You will mostly use the free webbasedsoftware Genepop (http://genepop.curtin.edu.au/) to estimate the parameters of interest.You will be graded on your abilities to interpret the dataset. The directory Assignment_2/Data/contains simulated datasets, each with a ####.gen extension. Please see DATA_ASSIGNMENTfor the specific file you are required to analyze!The lectures will provide you with all the needed know-how to answer the questions. There is aPDF demo of Genepop in the assignment directory.Setup:You are interested in studying the ecology and evolution of the mystical and glorious Egyptianscarab beetle, Khepri amrozayedi. After spending some time enjoying Kushari(https://en.wikipedia.org/wiki/Kushari) and contemplating the pyramids, you sailed down theNile to your study site near Luxor, in the Valley of the Kings(https://en.wikipedia.org/wiki/Valley_of_the_Kings).Here, you sampled 30 scarabs (15 males and 15 females; Scarabs are diploid) from 6 populations:Populations 1 to 3 and 4 to 6 were sampled West and East of the Nile river respectively. Map 1shows the location of the populations, and a matrix of geographic distances separating thepopulations. You genotyped each individual at 6 microsatellite loci. You tabulated all thegenotypes in a ####.gen file (rows are individuals, columns are loci), ready for analysis inGENEPOP.Map 1: Map of sampling sites of Khepri amrozayediDistance matrix (Km)POP 1 2 3 4 52 1.93 5.8 44 4.7 2.9 5.95 7.4 5.6 8.6 2.86 8 6.2 9.3 6.3 8.9Assignment 2, BIOL4390, Population Genetics, Prof. A. ZayedFeb 2020Your report will consist of the following:Data analysis 1: Summary TablesComplete the tables belowTable 1: Summary statistics (Notes, Hexp is expected FREQUENCY of heterozygous individuals)[add this to your report] (1 mark)LociL1 L2 L3 L4 L5 L6 Avg1 HexpFISHWE, p2 HexpFISHWE, p3 HexpFISHWE, p4 HexpFISHWE, p5 HexpFISHWE, p6 HexpFISHWE, pWest* HexpEast* HexpTotal* HexpComments: Hexp (Genepop > option 5), FIS (Genepop > option 5), and HWE test’s p value (Genepop> option 1) are automatically estimated. [Long way to estimate Hexp for the west region(populations 1 to 3), east region (populations 4 to 6) and the total population (1 to 6), you’ll needto average the allele frequencies at each locus for the populations in question (allele frequenciesare estimated using Genepop > option 5. e.g. to estimate Hexp for the West region at L1, find theaverage allele frequency for all the alleles at L1 using population 1 to 3, then estimate Hexp usingthe average allele frequencies). [Short way to estimate Hexp for the west region (populations 1 to3), east region (populations 4 to 6) and the total population (1 to 6)-> make new Genepop filesthat group relevant populations (e.g. west, east) together!!!.]Assignment 2, BIOL4390, Population Genetics, Prof. A. ZayedFeb 2020Table 2: Hierarchical F-statistics [add this to your report] (1 mark)L1 L2 L3 L4 L5 L6 AvgFSRFRTFST(You’ll do this manually. Refer to Lecture # 9. You’ll need to first estimate HS, HR, and HT , theaverage expected heterozygosity in subpopulations, regions, and the total populationrespectively; You would have already done most of these calculations for table 1)Table 2: Pairwise FST and Nm matrix [add this to your report] (1 mark)Comments: Pairwise FST is estimated using Genepop > option 6. It estimates Fst between two pairsof populations (given populations A and B, it estimates the proportionate reduction ofheterozygosity in the total A+B population compared to the average heterozygosity expected in Aand B alone). Estimate Nm manually (see Lecture 10). Place FST values above the diagonal, andNm values below he diagonalGraph 1 (1 mark) [add this to your report]: Examine the relationship between geographicdistance and genetic differentiation by plotting pairwise geographic distance and pairwiseestimates of FST. Examine the significance of this relationship using a linear regression analysis(Write the correlation coefficient, and the p-value of the regression on the graph). Try to usedifferent symbols or colors to denote pairwise comparisons within the west and east regionsversus pairwise comparisons between the west and east regions, but use all of the data pointsfor the correlation [Note: Linear regression assumes observations are independent this isviolated here because any one population is represented in several pairwise comparisons.Technically, a Mantel test should be used, however, for simplicity a linear regression analysis will befine, and the two generally give you the same result when the number of populations are large]Discussion: Provide a brief discussion of the following and use your analysis to supportyour claims.A. Mating system: How would you characterize the mating system of Khepri amrozayedi ?[random, inbreeding, or outbreeding] 2 marksJustify your answer in light of the population genetic evidence 4 marksPairwise FST / Nm matrixPOP 1 2 3 4 5 6123456Assignment 2, BIOL4390, Population Genetics, Prof. A. ZayedFeb 2020B. Population structure: What is the most important feature that influences patterns of gene flowbetween the sampled populations of Khepri amrozayedi.?[distance or geographic barrier] 2 marksJustify your answer in light of the population genetic evidence 4 marksC. You got extra funding so you genotyped an additional 200 microsatellite loci. 199 lociprovided similar estimates to the six studied herein. One locus showed a peculiar pattern alleastern populations were fixed for one allele, while all western populations were fixed foranother allele? What is FST for that locus? [1 mark] What is the most likely evolutionary processthat is causing this locus to be different from the others? Can you give an example? [3 marks]
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