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MMPH6005/SBMS7100
Assignment 3
Due: December 15, 2024 (Sun) 23:59
Submit through Moodle assignment dropbox
1 Calculate the distance between these two sequences using the p-distance and the Jukes and Cantor and Kimura methods.
>A
CGCAAACGATTTGCAGACCAAGAACTGGGTGATGCC
>B
AGGAAGCTGCTCAGCATGAGAAACATGTGTGATGCT
2 Which method is more likely to be accurate and why?
3 Based on the distance matrix shown, the tree above was formed by the newick tree file description below. Except that the format given is incorrect (whoops!). Please help the lecturer out and correct the tree file.
((D:5.0,E:6.0):4.0,C:9.0 (A:10.0,B:12.0:20.0);
4 That tree example was for an unrooted tree. Please say how many different rooted trees you could make for this tree (based on branching order, not changes in branch lengths).
5 That tree (again) was created by the neighbour joining algorithm. What differences would there be if UPGMA had been used on that distance matrix?
6 Show the calculation under UPGMA to take the matrix on the left to the one on the right based on the original matrix above and the steps of UPGMA (this is part of UPGMA on the matrix above).Using a BLASTN search of the nr database with sequence B above, the best 50 sequence matches were returned and a tree made using the NCBI “Distance tree of results” feature.
The sequences and tree were saved (with a bit of judicious editing of the sequence titles).
The tree is shown below and the files are available on moodle to download and display in MEGA, figtree or other software.
7 Where do you think the root of the tree should be and what is your reason (method for rooting a tree) for that choice? Your explanation is important (what made you think that way) – your choice of root doesn’t necessarily have to be right).
8 What is your next best choice and why?
9 Why do you think the branch at “D” is very long?
10 A similar BLASTN search process was done with sequence A and the alignments were combined to give the tree below. How does this help the choice of root for the sequence B related tree above? Why would or wouldn’t you alter your choice of root above?
11What biological entity do you think sequences A and B were from? On what basis?
You can use MEGA and figtree to make and/or show trees. If you cant use these, the link below will make distance metric based trees.
https://www.ebi.ac.uk/jdispatcher/phylogeny/simple_phylogeny (Note: Phylip = Newick)0.04
A/eurasian coot/Shandong/W4446/2020(H10N4)
A/duck/Vietnam/HN5983/2019(H9N9)
A/Tawny frogmouth/Western Australia/AS-21-1823-0007/2021(H10N7)
A/chicken/Egypt/N16946C/2019(H9N2)
A/chicken/Egypt/A17969/2019(H9N2)
A/chicken/Egypt/F17124D/2019(H9N2)
A/chicken/Taipei/17050008-3/2017(H5N8)
A/duck/Pingtung/15A03399-1-10T/2015(H5N2)
A/duck/Yunlin/17A0086/2017(H5N2)
A/duck/Vietnam/HU5 -483/2016(H10N6)
A/duck/Bangladesh/46157/2020(H5N1)
A/herring gull/Iceland/2177/2012(H6N7)
A/greylag goose/Iceland/5878/2016(H6N8)
A/Cormorant A/eider/USA
/Namibia /22-031265
/141/2022
-003(H
/2022
5N1
(
)
H5N1)
A/Green-winged Teal/North Carolina/22-003830-003/2022(H5N1)
A/Turkey/South Dakota/22 -009980-001/2022(H5N1)
A/Bald Eagle/Illinois/22-011028-001/2022(H5N1)
A/chicken/Minnesota/22 -012932-001/2022(H5N1)
A/Bald Eagle/Minnesota/22-011586-002/2022(H5N1)
A/duck/Hokkaido/119/2003(H7N1)
A/duck/Buryatia/664 -5465/1988(H3N1)
A/mallard/Vermont/AH0188063/2021(H5N3)
A/Sanderling/Delaware/507/2021(H10N3)
A/Ruddy Turnstone/DE/777/2022(H11N8)
A/ruddy turnstone/DE/577/2023(H10N7)
A/northern pintail/Alaska/AK19-534/2019(H3N8)
A/Backyard bird/Michigan/22-012454-002/2022(H5N1)
A/Thalasseus acuflavidus/IlhaCompridaBR/2280-N/2023(H5N1)
A/Chiloe wigeon/OHiggins/240893-2/2023(H5N1)
A/chicken/Montana/23-030330-002-original/2023(H5N1)
A/cattle/Texas/24 -009028-009/2024(H5N1)
A/cattle/TX/24-019890-002-original/2024(H5N1)
A/cattle/ID/24 -017478-002-original/2024(H5N1)
A/cattle/MN/24 -017652-007-original/2024(H5N1)
A/environment/USA/CO -UW-9084466/2024(H5N1)
A/cattle/SD/24-021715-006-original/2024(H5N1)
A/chicken/Bangladesh/40619/2019(H9N2)
A/chicken/Bangladesh/45697/2020(H9N2)
A/chicken/Bangladesh/49758/2021(H9N2)
A/canine/China/HN3/2018(H3N2)
A/canine/Nanjing/20170515-25/2017(H3N2)
A/environment/Jiangxi/2.05 SRXZWS029-E/2017(H6N6)
A/pheasant/South Korea/N13-010/2013(H3N2)
A/chicken/Korea/5/2009(H6N2)
A/chicken/Egypt/CL69/2013(H5N1)
A/duck/Vietnam/QN3335/2016(mixed)
A/chicken/Vietnam/LBFecal8LS/2019(H5N6)
A/mink/China/191/2019(H5N6)
A/chicken/China/NN2/2011(H9N2)
A/aquatic bird/Cheongju/180/2007(H2N4)
A/duck/Kinmen/05WB11 -798-7-12-E1/2005(H3N8)
A/duck/Iwate/301007/2012(H7N1)
A/duck/Hokkaido/W87/2007(H10N2)
A/duck/Kinmen/05WB11 -773-11-15-E1/2005(H3N8)
A/duck/Jiangsu/S1665/2015(H5N3)
A/duck/Hokkaido/WZ75/2017(H6N2)
A/equine/Jilin/1/1989(H3N8)
A/duck/Fujian/6.22 FZHX06112 -O/2017(mixed)
A/duck/Fujian/1.25 FZHX0014-O/2018(H7N3)
A/duck/Fujian/1.25 FZHX0014-C/2018(H7N3)
A/duck/Fujian/1.25 FZHX0049-O/2018(H7N3)
A/chicken/Fujian/03.15 FZHX0001-C/2018(H7N3)
A/duck/Fujian/1.25 FZHX0012-O/2018(H7N3)
A/duck/Fujian/1.25 FZHX0003-O/2018(H7N3)
A/duck/Fujian/1.25 FZHX0007-O/2018(H7N3)
A/duck/Vietnam/HU9 -194/2018(H6N6)
A/environment/Chile/C63057/2023(H6N5)
A/environment/Chile/C63153/2023(H12N5)
A/Common Goldeneye/Wisconsin/18OS3317/2018(H2N3)
A/Common Goldeneye/Wisconsin/17OS5804/2017(H4N8)
A/Common Goldeneye/Wisconsin/17OS5560/2017(H4N8)
A/turkey/Indiana/1403 -1/2016(H7N8)
A/northern pintail/Alaska/AK18-WB1-098A/2018(H3N6)
A/chicken/Aguascalientes/CPA -08545-19/2019(H5N2)
A/chicken/Aguascalientes/CPA -08115-19/2019(H5N2)
A/chicken/Puebla/CPA-03924-19/2019(H5N2)
A/chicken/Puebla/CPA-01572-18/2018(H5N2)
A/chicken/Guanajuato/CPA-04382-19/2019(H5N2)
A/chicken/Queretaro/CPA -04112-19/2019(H5N2)
A/chicken/Jalisco/CPA-03604-19/2020(H5N2)
A/chicken/Jalisco/CPA-04262-19/2019(H5N2)
A/chicken/San Luis Potosi/CPA-05885-19/2019(H5N2)
A/chicken/Queretaro/CPA -02177-17/2017(H5N2)
A/chicken/Veracruz/CPA -04704-17/2017(H5N2)
A/chicken/Guanajuato/CPA-17726-17/2017(H5N2)
A/chicken/Morelos/CPA-02447-17/2017(H5N2)
A/chicken/Morelos/CPA-05154-17/2017(H5N2)
A/chicken/Jalisco/LVVX17186 -2/2017
(H5N2)
A/chicken/Veracruz/CPA -05600-17/2017(
H5N2)
A/Gallus gallus/Tepatitlan de Morelos/CPA-04948-23/2023(H5N2)
A/chicken/Mexico/1863/2019(H5N2)
A/chicken/Jalisco/8-4-03/2020(H5N2)
A/chicken/Veracruz/CPA -21377-17/2017(H5N2)
A/chicken/Queretaroa/CPA -11747-18/2018(H5N2)
A/chicken/Aguascalientes/CPA -07048-19/2019(H5N2)
A/chicken/Aguascalientes/CPA -03203-19/2019(H5N2)
A/chicken/Guanajuato/CPA-07267-19/2019(H5N2)
A/chicken/Guanajuato/CPA-07268-19/2019(H5N2)
A/chicken/Guanajuato/CPA-05981-19/2019(H5N2)