BS1008 - Plant Phylogenetics Practical (data matrix and sites for analysis are below) update March 2013

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The references: http://taxonomy.zoology.gla.ac.uk/teaching/CompleatCladist.pdf

http://www.gwu.edu/~clade/faculty/lipscomb/Cladistics.pdf are relevant

www.onezoom.org is an interesting tool for exploring relationships between tetrapod animal species.

The Herbarium film is here:

 

The Data Matrix for Leaf Characters:

To be able to use the same program for DNA and character analyses, the character states for the leaves have been coded as 0=A, 1=T, 2=G, 3=C; '?' is used for uncertain/variable states.

7 8
Arabidops.AAAAAAAA
Q.petrea..ATATTTTA
Q.robur...ATTTATTA
Q.faginea.AGATTTTA
Q.ilex....TAAATGAT
Ilex x altTAAAAATT
Osmanthus.?GAAAGAT

The online version of PHYLIP

This program is normally run on your own computer, but these organizations have kindly made available an on-line version.

Use the DNA Parsimony program: available from http://www.es.embnet.org/Services/

at http://www.es.embnet.org/Services/MolBio/phylip/dnapars.html

(Another version is at http://www.trex.uqam.ca/index.php?action=inference&project=trex The following have worked in the past but seem not to work 22/2/2013:http://bioweb2.pasteur.fr/phylogeny/intro-en.html http://bioportal.bic.nus.edu.sg/phylip This seems not to work 10 March 2011; 22/2/2013 others on the "PHYLIP server service" section of http://evolution.genetics.washington.edu/phylip/phylipweb.html also do not seem to work).

The DNA sequence data:

7 663
Rice%%%%%%GGGGATATGGCGAAATCGGTAGACGCTACGGACTTGATTGTATTGAGCCTTGGTATGGAAACCTGCTAAGTGGCAACTTCCAAATTCAGAGAAACCCTGGAATTAA??AAAAGGGGCAATCCTGAGCCAAATCCATGTTTTGAGAAAACAAGC???GGTTCTCGAACTAGAACCCAAAGGAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACGAATCGAGTTAATTACGTTGTGTTGCTAGC?????GGAA??CTCCCTTCTAAATTAGGG?AAAGAAGGGCTTTCGAAATCTAATACCACGTATAGATACTGGCATAG?????CAAACGATTAATCACAGAACTCATATCATAATATAGGTTCTTTAATTCTTTTT????????AAAATGAAAATAGGAATGATTATGAAATAGAAAATTCATAATTTTTTTAGAATTGTTGTGAATCCATTCCA?????????????ATCGAATATTGAGTAATCAAATCCTTCAATTCATAGTTTTCGAAATCTTTTTAAAAGCGGATTAATCGGACGAGGATAAAGAGAGAGTCCCATTCTACATGTCAATACTGACAACAATGAAATTTGTAGTAAAAGCAAAATCCGTCGACTTTCTAAGTCGTGAGGGTTCAAGTCCCTCTATCCCCA
Q.petrea..GGGGATATGGCGAAATCGGTAGACGCTACGGACTTAATTGGATTGAGCCTTGGTATGGAAACTTACCAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAATTAA???AAATGGGCAATCCTGAGCCAAATCC?TATTTTACGAAAACAAATAAGGGTTCAGAAGAAAGCGAGAATAAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAGTGGGGTTGACTTCTTTACGTTATTACATTAACGTAATCCTTATATCAAAACTACAGAAAG???????GATAAACCTATATACATACGTATATGTACTGAAATCCTATCTCAAATGATTAATGACGACCC???????????????GAATCTTTATTTATTTATATTTCTATAAATAATAAATAAAAATC???????????????????????????GAAAGAGTTGTTGTGAATCGATCCAA?ATTGAAGAAAGAATCGACTATTTATTAATAAA????????????????????????????????????????ATTTATCGTACGAGAATAAAGATAGAGTCCCATTCCACACGTCAATACCGACAAGAATGAAATTTATAGGAAGAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA
Q.robur...GGGGATATGGCGAAATCGGTAGACGCTACGGACTTAATTGGATTGAGCCTTGGTATGGAAACTTACCAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAATTAA???AAATGGGCAATCCTGAGCCAAATCC?TATTTTACGAAAACAAATAAGGGTTCAGAAGAAAGCGAGAATAAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAGTGGGGTTGACTTCTTTACGTTATTACATTAACGTAATCCTTATATCAAAACTACAGAAAG???????GATAAACCTATATACATACGTATATGTACTGAAATCCTATCTCAAATGATTAATGACGACCC???????????????GAATCTTTATTTATTTATATTTCTATAAATAATAAATAAAAATC???????????????????????????GAAAGAGTTGTTGTGAATCGATCCAA?ATTGAAGAAAGAATCGACTATTTATTAATAAA????????????????????????????????????????ATTTATCGTACGAGAATAAAGATAGAGTCCCATTCCACACGTCAATACCGACAAGAATGAAATTTATAGGAAGAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA
Q.faginea.GGGGATATGGCGAAATCGGTAGACGCTACGGACTTAATTGGATTGAGCCTTGGTATGGAAACTTACCAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAATTAA???AAATGGGCAATCCTGAGCCAAATCC?TATTTTACGAAAACAAATAAGGGTTCAGAAGAAAGCAAGAATAAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAGTGGGGTTGACTTCTTTACGTTATTACATTAACGTAATCCTTATATCAAAACTACAGAAAG???????GATAAACCTATATACATACGTATATGTACTGAAATCCTATCTCAAATGATTAATGACGACCC???????????????GAATCTTTATTTATTTATATTTCTATAAATAATAAATAAAAATC???????????????????????????GAAAGAGTTGTTGTGAATCGATCCAA?ATTGAAGAAAGAATCGAATATTTATTAATAAA????????????????????????????????????????ATTTATCGTACGAGAATAAAGATAGAGTCCCATTCCACACGTCAATACCGACAAGAATGAAATTTATAGGAAGAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA
Q.ilex....GGGGATATGGCGAAATCGGTAGACGCTACGGACTTAATTGGATTGAACCTTGGTATGGAAACTTACCAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAATTAA???AAATGGGCAATCCTGAGCCAAATCC?TATTTTCCGAAAACAAATAAGGGTTCAGAAGAAAGCGAGAATAAAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAGTGGGGTTGACTTCTTTACGTTATTACATTAACGTAATCCTTATATCAAAACTACAGAAAG???????GATAAACCTATATACATACGTATATGTACTGAAATCCTATCTCAAATGATTAATGACGACCC???????????????GAATCTTTATTT????ATATTTCTATAAATAATAAATAAAAATC???????????????????????????GAAAGAGTTGTTGTGAATCGATCCAA?ATTGAAGAAAGAATCGAATATTTATTAATAAA????????????????????????????????????????ATTTATCGTACGAGAATAAAGATAGAGTCCCATTCCACACGTCAATACCGACAAGAATGAAATTTATAGGAAGAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA
Ilex x altGGGGATATGGCGAAATCGGTAGACGCTACGGACTT????????????????GGTATGGAAACCTACTAAGTGATAACTTTCAAATTCAGAGAAACCCTGGAATTATTAAAAATGGGCAATCCTGAGCCAAATCC?TATTTTCCGAAAACAAA?????????????????GCGAAAAT?CAAAAAGGATAGGTGCAGAGACTCAACGGAAGCTGTTCTAACAAATAGAGCTGACTGTGTTGCATTGGTAGA?????GGAATCCTTCTATCGAAACCTCAGAAAGGATGAAGGATAAACCTATATAC??????ATACGTACTCAAATACCATATCAAATGATTAATGACGACCC???????????????GAATCTGTATCTAT??ATTTTTATATGAAAAATA??????????????????????????????????????GAAGAATTGTTATGAATCGATTCTACATTAAAGAAAGAATCGAATATTCATTGATCAAATCATTCACTCCATAGTCTGATAGATCTTTTGAGGAACTGATTAATCGGACGAGAATAAAGATAGAGTCCCATTCTACATGTCAATACCGGCAACAATGAAATTTATAGTAAGAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA
Osmanthus.GGGGATATGGCGAAATCGGTAGACGCTACGGACTTAATTGGATTGAGCCTTGGTATTGAAACCTACTAAGTGGTAACTTTCAAATTNANAGAAACCC?GGAATTAATAAAAATGGGCAATCCTGAGCCAAATCC?TGTTTTCCCAAAACAAA????GGTTCAGAAAG???????????AAAAAAGGATAGGTGCAGAGACTCAATGGAAGCTGTTCTAACAAAATGGAGTGGC????CTGCGTTGGTAGA?????GGAATCTTTCCATCGAAACTTCAGAAAGGATGAAGGATAAACGTATATAT???????????????TGAATACTATATCAAATGATTAATGACGACTC???????????????GAATCTCTATCTGTATTTTTTTATATGAAAAATG??????????????????????????????????????GAAGAATT??????????GATTCCACATTGAAGAAAGAATCGAATATTCATTGATCAAATCATTCACTCCATAGTCTGATAGATCTTTTAAAGAACTGATTAATCGGACGAGAATAAAGATAGAGTCCCATTCTACATGTCAATACCGCCAACAATGAAATTTATAGTAAAAGGAAAATCCGTCGACTTTAGAAATCGTGAGGGTTCGAGTCCCTCTATCCCCA

 

An advanced course but along similar lines to this one is posted at: http://rogerlab.biochemistryandmolecularbiology.dal.ca/lab3_2011.html

by Dr Andrew Roger, Dakhousie University, Halifax, Canada, http://rogerlab.biochemistryandmolecularbiology.dal.ca/index.php

as part of his bioinformatics course: http://rogerlab.biochemistryandmolecularbiology.dal.ca/bioc4010.php

Click on Lab 3 to see the Phylogenetics Lab (but the course slides are not available).

 

Some of the best references on phylogenetics are available on the web, and usually are associated with lists of computer programs. PHYLIP, the Phylogeny Inference Package used here, was written by Joe Felsenstein. He maintains an extensive web site that offers free downloads of PHYLIP software, documentation (which includes the applications of the methods and the associated mathematical algorithms). and information about 160 other phylogeny software packages. http://evolution.genetics.washington.edu/phylip.html

Two excellent books are:

The Compleat Cladist: A Primer of Phylogenetic Procedures, by E. O. Wiley, D. Siegel-Causey, D. R. Brooks, V. A. Funk, University of Kansas Museum Of Natural History Special Publication No. 19, 1991.
http://taxonomy.zoology.gla.ac.uk/teaching/CompleatCladist.pdf

 

And

Basic guide to phylogenetic analysis (using cladistics), by Diana Lipscomb, George Washington University is at http://www.gwu.edu/~clade/faculty/lipscomb/Cladistics.pdf

 

The Tree of Life Project at the University of Arizona gives a good overview of the overall process of taxonomy and is found at http://tolweb.org .

 

 

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