Lab 11 Data Sheet

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Jun 5, 2024

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ELTEEIEYT LA A B AR R AR RCECERRRERERRN LABORATORY 11: DATA SHEET Name:_Addana. Sondnez Lab Partner(s):_Savannan Date: 412212024 Exercise | (p.113) 1. Below is an alignment of a portion of the mtDNA genome from several humans and chimpanzees. The first human sequence is shown in full and the other sequences are compared to it. A dot indicates the place where the base pair of the sequence matches the first sequence (Human #1). The nucleotide is indicated where there is a mismatch when compared to the Human #1 sequence. A dash indicates a base pair is missing (a deletion) when compared to the Human #1 sequence. Human #1 1 CCCCCCCCAT GCTTACAAGC MGTACAGCA ATCAACCTTC AACTATCACA CATCAACTGC AACTCCAAAG CCACCCCTCA CCCACTAGGA TACCAACAAA 100 Chimp #1 Chimp #2 Chimp #3 Chimp #4 Chimp #5 a. Give the base pair number for a SNP marker that is fixed between human and chimps. IZ ‘ase pair b. Give the base pair number for a SNP marker that would be useful for studying population variation within humans. 4 base pair Give the base pair number for a SNP marker that would be useful for studying population variation within chimps. UT base pair Laboratory 117 Studying Evolutionary Genetics with Mitochondrial DNA 117
2. Using the alignment provided by your lab instructor, collect data about COXT DNA sequence divergence in the eukaryotes. Total length of COX7 gene segment: ___ 50 bp human | fruirfly | Hiopio | chirmp | mouse | Yeast human, e 1® g 5 (p |7 fuitflu | 0.30 - \S 19 13 1z Tilapia | 0.0 0. 20 - 10 7 P Chme | ©.l10 *| 0.3% | 0.20 - \0 17 Meust | 0.2 0.20 | 0.4 | 0.20 - 17 | least | o34 o.24 | 032 | ©0.32 | O.34 - 3. Create an UPGMA tree using the nucleotide sequence distances you calculated above. You are welcome to use the whiteboards to create a draft of your tree before filhngm your completed tree below. (0.30 40.33 2 0.2 0Lz +222:0.588 —— 0.003)| 00 Huma n 0.05 Chirmp 0 L ,.8‘ Mousc 0.18% 0.083 -“\q?\. a r 0. VQQS“ 4. Using the alignment provided by your lab instructor, collect data for COX1 protein sequence divergence in the eukaryotes. Total length of COX1 protein segment: 100 aa C0\3 rait Fly Homeo | FowFly | Tilopia | Chimp | Mouse Yeay: Hurmans T e 15 \ | L . 37 Futfy | Ous - 2\ Y 5 34 Topia | O\ - | 0.2 ) \Z <l 31 comp | o.01e| 0.4 | 0.2 - n 30 Mmouse | 0.0pe| 0.5 0.09 0.01' T 37 Yeast | 0.z | 0.34 | 0.31 | 0.30 | 0.37 - 118 studying Evolutionary Genetics with Mitochondrial DNA | Laboratory 11 ARARIRIRARARARL TRV \ \ AR RMEREREREEARRB annonananNannnar
5. Create an UPGMA tree using the amino acid sequence distances you calculated. You are welcome to use the whiteboards to create a draft of your tree before filling in your completed tree below. 0.0\ /.9 = 0.00% . 00k, Huamans . Mous ¢, 3;'1 ¥0.34 YO.37+0.3¢ t031 o 2. . . ” Bl 5 = 0.3(s2. o Fruny F) 0.342 - 2= 0,1g| b& Yeast 6. Did you get the same phylogeny using the gene and gene product? Which tree seems more reliable? (Hint: Did you look at the same amount of nucleotides in both trees?) Noi the Phylogeny isnt the same a3 the qene and Que product because 4ne decond UPGMA tree 15 different. The 4ree that Seens More celvble WoUId be 4ne amino acid Sequence tree. 7. Circle the node of the tree in question 3 that represents the common ancestor of all vertebrates. Circle the node in question 5 that represents the common ancestor of all eukaryotes. 8. The divergence time between humans and fruit flies is estimated at 800 million years. Use this as a calibration point for the COX1 protein molecular clock (though we could also have used the gene sequence), to determine the following: 15/800 = 0.\Q °/o D % seq diverg/__|Q0 _ mill years of diverg = _0. 14 % change per million years 9. Using the rate you calculated in question 8, calculate the divergence time between two other taxa. How would your answer change if you were calculating to the most recent common ancestor of those two taxa? 100 miy| years/o.la . Change per milhcn years = LOO mihen geat® This wouid change the calcuiaricns of fhe most rccen+ Py having mimmal amount of time & %o of sequence diveraence. 10. Why do you think COX1 is often used to study deep phylogenetic relationships between organisms? because ir g o type oF genc thar is hignly consecved, “heh maues it casier +o identify the orgomsms, [abioratory 11| Studying Evolutionary Genetics with Mitochondrial DNA 119 CoX\ is offen used to study deCR Phylogeneric faatensnips
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11. Does the sequence divergence data you collected represent evidence for a common ancestor of these living things? Yesr T elve ¥ne sequence dwergence dora Cllectred to represent evidence as a. Corntan ances{ee. Exercise Il (p.113) 12. a. Whatis your sample ID# (written on p.100 or somewhere in your lab manual)? ifl_ b. Which haplogroup did MITOMAP identify for your mtDNA? __ A2 13. a. # of differences (variants) between your mtDNA and the Reference Sequence _‘{_ b. Sequence divergence between your mtDNA and the Reference Sequence Y 14. Using a molecular clock rate of 6% sequence divergence per million years, calculate the divergence time between your sequence and the Reference Sequence. Then estimate the age of the common ancestor between your haplogroup and the Reference Sequence, or mtEve. Show your work. 18] «co u.s/ ¥ T0.18 mi\lhvcn gears or T%0,000 Tt e Years LLS °fe - Uo/a X = 1801000 /3 - 375,0c0 uears o commMen ancestoc 1% diffecences 120 Studying Evolutionary Genetics with Mitochondrial DNA | Laboratory 11 €Y gV g0 < - S‘\ (? (4\ i‘ ‘«‘ i \ \ \ | S \ \ IR T T T T T U . . . N \ 1 apeoccecoo00 4 nn fpprNNRRREAAARNN DD ne a

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