You must type this and all other homework assignments. Do not e-mail the assignment to me; turn it in early (at 322 Wolf) for a foreseeable absence, or turn it in late after an unexpected absence from class.
Here are some practice questions for the exam. If the answer is "one-way anova," you must specify Model I or Model II; if the answer is "nested anova," you must specify Mixed Model or Pure Model II.
1. You travel to Canada and observe the snow goose, Chen caerulescens. Snow geese come in two color morphs, white or blue. You want to know whether the blue geese and white geese prefer different areas. You go to four different lakes, and at each lake you record the first 100 snow geese you see. You see 35 blue geese at Lac Oie, 24 blue geese at Lago de Ganso, 19 blue geese at Lake Anser, and 44 blue geese at Pokebutt Pond. What test should you use?
2. Blue geese and white geese mate with each other (the polymorphism is caused by two alleles at a single gene); you want to know how random the mating is. At each of the four lakes, you find a few dozen blue/white mated pairs and record how many have a blue male and white female, and how many have a white male and blue female. What test should you use?
3. You want to know whether the plumage color affects the number of offspring. You go to Lake Anser and find 19 nests with both blue parents, 36 nests with a blue male and a white female, 33 nests with a white male and blue female, and 49 nests with both white parents. You count the number of eggs in each nest. What test should you use?
4. You want to know whether the plumage color affects the weight of offspring. You go to Lake Anser and find 19 nests with both blue parents, 36 nests with a blue male and a white female, 33 nests with a white male and blue female, and 49 nests with both white parents. You weigh every gosling in each nest. What test should you use?
5. Students in my section of BISC413, Advanced Genetics Lab, collected data on codon bias in different genes in Drosophila melanogaster. Codon bias is when some synonymous codons are used more often than others; for example, TTC and TTT both code for phenylalanine, but in Drosophila, TTC is more common. One measure of codon bias is called the Codon Bias Index, or CBI. Each student found the CBI for several genes in a region of a chromosome. At the bottom of the page are data for three regions of the X chromosome and three regions of the third chromosome. Analyse the data using a nested anova, and write a couple of sentences interpreting the results. Then pool together all of the X-chromosome data, pool together all of the third-chromosome data, and analyze using a single-classification anova (or a t-test). Compare the results of the two tests; what does analyzing the data with a nested anova tell you that you wouldn't get from a single-classification anova?
(Note--please don't copy these data into a spreadsheet by retyping them. Instead, copy the whole data set from this web page, paste into a blank spreadsheet, then use the "Text to columns" command to separate the numbers into different columns. You can then copy the numbers from the blank spreadsheet into the nested anova spreadsheet.)
Chromosome Region Gene CBI
1 7D singed 0.366
1 7D CG1409 0.224
1 7D CG15326 0.165
1 7D CG2175 0.125
1 7D CG15327 0.202
1 7D CG15325 0.264
1 7D CG1543 0.329
1 7D CG15333 0.066
1 7D CG2233 0.125
1 7D CG2252 0.205
1 7D CG1560 0.296
1 13F sd -0.081
1 13F chc 0.282
1 13F CG32582 -0.224
1 13F CG8565 0.142
1 13F Aats-arg 0.161
1 13F CG8509 0.191
1 13F PGRP-LE 0.17
1 13F CG15602 0.114
1 16A CG8611 0.276
1 16A CG5488 0.246
1 16A CG5445 0.253
1 16A CG8661 0.395
1 16A CG8664 0.612
1 16A CG5424 0.359
1 16A CG5529 0.286
3 75C thick veins 0.205
3 75C virile -0.012
3 75C white 0.358
3 75C wrinkled -0.083
3 75C zerknult -0.102
3 75C zipper 0.271
3 75C CG7320 -0.126
3 93C CG5871 0.266
3 93C CG3337 0.15
3 93C CG5874 0.235
3 93C ebony 0.401
3 93C CG5892 0.138
3 93C ETHR 0.416
3 93C Rab1 0.18
3 94D Heldout 0.248
3 94D gem 0.248
3 94D mei-w68 0.147
3 94D CG4656 0.177
3 94D Lnk 0.133
3 94D Fbp1 0.365
3 94D Rp513 0.614
6. McDonald et al. (1991) compared the shell morphology of three species of marine mussel, Mytilus edulis, Mytilus galloprovincialis and Mytilus trossulus, from various locations around the world. The three species can be distinguished using genetic characters, but they are very difficult to identify using just the shells. One of the characters that does show some difference among the species is the length of the anterior adductor muscle scar, or AAM length. Here are AAM lengths (standardized by dividing by total length) for a bunch of mussels. Analyze the data using a nested anova. Graph the means for the locations, grouped by species (you do not need to add error bars). Based on the results of the anova, if you were to do a followup study in which you measured 1000 more mussels, would you sample a few mussels from a lot of locations for each species (which would be a lot of work), or a large number of mussels from a small number of locations (which would be easier)?
species location ID number AAM edulis Aarhus 26 0.150 edulis Aarhus 27 0.179 edulis Aarhus 28 0.164 edulis Aarhus 29 0.129 edulis Aarhus 30 0.147 edulis Aarhus 31 0.157 edulis Aarhus 32 0.128 edulis Aarhus 33 0.166 edulis Aarhus 34 0.119 edulis Aarhus 35 0.167 edulis Aarhus 36 0.190 edulis Aarhus 37 0.160 edulis Magdalen 1280 0.103 edulis Magdalen 1280 0.107 edulis Magdalen 1280 0.131 edulis Magdalen 1280 0.108 edulis Magdalen 1280 0.136 edulis Magdalen 1280 0.125 edulis Magdalen 1280 0.116 edulis Magdalen 1280 0.116 edulis Magdalen 1280 0.115 edulis Magdalen 1280 0.133 edulis Magdalen 1280 0.121 edulis Magdalen 1280 0.111 edulis Shinnecock 1526 0.118 edulis Shinnecock 1529 0.115 edulis Shinnecock 1533 0.128 edulis Shinnecock 1534 0.108 edulis Shinnecock 1535 0.117 edulis Shinnecock 1536 0.123 edulis Shinnecock 1539 0.106 edulis Shinnecock 1540 0.108 edulis Shinnecock 1541 0.129 edulis Shinnecock 1547 0.105 edulis Shinnecock 1548 0.119 edulis Shinnecock 1549 0.139 gallo HongKong 3 0.114 gallo HongKong 4 0.100 gallo HongKong 12 0.078 gallo HongKong 24 0.091 gallo HongKong 25 0.093 gallo HongKong 27 0.092 gallo HongKong f20 0.122 gallo HongKong f26 0.115 gallo HongKong m14 0.089 gallo HongKong m15 0.094 gallo HongKong m22 0.066 gallo HongKong m23 0.086 gallo SanDiego m110 0.060 gallo SanDiego m16 0.084 gallo SanDiego sd17 0.085 gallo SanDiego sd21 0.077 gallo SanDiego sd22 0.101 gallo SanDiego sd28 0.083 gallo SanDiego sd30 0.073 gallo SanDiego sd32 0.072 gallo SanDiego sd34 0.072 gallo SanDiego sd809 0.083 gallo SanDiego sd810 0.092 gallo SanDiego sd812 0.067 gallo Venice 1 0.090 gallo Venice 2 0.062 gallo Venice 3 0.049 gallo Venice 4 0.084 gallo Venice 5 0.061 gallo Venice 7 0.071 gallo Venice 8 0.072 gallo Venice 9 0.050 gallo Venice 10 0.096 gallo Venice 11 0.088 gallo Venice 12 0.096 gallo Venice 13 0.063 trossulus Magadan 2228 0.069 trossulus Magadan 2229 0.068 trossulus Magadan 2231 0.083 trossulus Magadan 2234 0.075 trossulus Magadan 2235 0.078 trossulus Magadan 2238 0.073 trossulus Magadan 2239 0.103 trossulus Magadan 2240 0.076 trossulus Magadan 2241 0.066 trossulus Magadan 2243 0.068 trossulus Magadan 2244 0.091 trossulus Magadan 2249 0.070 trossulus Newport 226 0.072 trossulus Newport 228 0.091 trossulus Newport 230 0.075 trossulus Newport 234 0.065 trossulus Newport 235 0.091 trossulus Newport 238 0.074 trossulus Newport 239 0.082 trossulus Newport 241 0.084 trossulus Newport 244 0.087 trossulus Newport 245 0.085 trossulus Newport 247 0.067 trossulus Newport 249 0.066 trossulus Posyet 2251 0.096 trossulus Posyet 2254 0.101 trossulus Posyet 2255 0.121 trossulus Posyet 2256 0.108 trossulus Posyet 2257 0.103 trossulus Posyet 2265 0.116 trossulus Posyet 2266 0.107 trossulus Posyet 2268 0.097 trossulus Posyet 2268 0.100 trossulus Posyet 2271 0.119 trossulus Posyet 2274 0.117 trossulus Posyet 2275 0.092 trossulus Petersburg 901 0.097 trossulus Petersburg 905 0.106 trossulus Petersburg 915 0.115 trossulus Petersburg 928 0.121 trossulus Petersburg 929 0.135 trossulus Petersburg 930 0.105 trossulus Petersburg 943 0.106 trossulus Petersburg 946 0.082 trossulus Petersburg 948 0.106 trossulus Petersburg 955 0.097 trossulus Petersburg 961 0.102 trossulus Petersburg 963 0.114
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This page was last revised October 18, 2007. Its URL is http://udel.edu/~mcdonald/stathw7.html