Phylogenetic Analysis

Report by Rachelle Jenine D. Abuel Biochem 170 @Sir Junny_neutron #classhug

The Theory of Evolution

#evolutionistheprinciple

Charles Darwin father of evolution A gradual process in which something changes into a different and usually more complex or better form Life originated from a universal common ancestor Survival of the fittest

Systematics
#systematicsisthefoundation

Science of comparative biology to describe taxic diversity and reconstruct hierarchy trough phylogenetic relationships Can be a basis of taxonomic classification

Phylogenetics
#phylogeneticsisthelesson

Science of estimating the evolutionary past based on DNA, RNA or protein sequences Used to infer and estimate the commonality between species

Phylogenetic Terminology
#phylogeneticterms

Phylogenetic tree
Visual representation of relationships Horizontal distances may have meaning

Branches connects the nodes Nodes point of diversion

Phylogenetic Terminology
#phylogeneticterms

Homologues members of the same node; can be paralogues or orthologues Paralogues

Members of multi-gene families Arises from gene duplication

Orthologues
Vertically-transmitted Phylogeny traces that of their host lineage

Phylogenetic Terminology
#phylogeneticterms

Groups
Monophyletic (Clade)
All are derived from a common ancestor and have inherited a set of unique common traits

Paraphyletic
a group excluding some of its descendants (e.g., animals excluding humans)

Polyphyletic
distantly-related superficially resembling one another retaining a common primitive characteristic

Methods of Analysis
#howtoanalyzephylogenetics

Sequence alignment Assessing phylogenetic signal Choosing mode of analysis Construction of phylogenetic tree Assessing phylogenetic reliability

Methods of Analysis
#howtoanalyzephylogenetics

Two analysis signals

Distance-based Character-based

Two modes of approaches

Global Alignment (full stretch of sequences) Local Alignment (only regions of similarity)

Applications for Analysis

#PHYLIPcanbeusedwithouttheinternet

PHYLIP (Phylogenetic Inference Package)

Group of executable files that cover almost all aspects of phylogenetic analysis Developed by Joe Falsenstein FREEEEEEsoftware, but is so C-based type line command process (OH, THE HORROR OF COMSCI 110!)
http://evolution.genetics.washington.edu/phylip.html

Classmate: (in conyo tone) Cheline, how can I get relative information about the relationship of a rabbit from a human from an opossum from a chicken and from a frog? Cheline: oi, lesson ko yan. MADALI LANG. USING PHYLIP! Teka. Bibili muna ako ng pantalon. Tatlo. Dapat galing sa penshoppe.

PHYLIP dnadist Steps

#PHYLIPdnadistPreparationStep

1. Download the package from the website. Extract. 2. You need a sequence data in Phylip format.
Copy-paste sequence in http://www.ebi.ac.uk/cgibin/readseq.cgi to convert sequence to phylip format Save it to the same folder as your executable file.

Before downloading

PHYLIP dnadist Steps

#PHYLIPdnadistExecutionStep

3. Double-click on dnadist executable file and a prompter will ask you for a file (default: infile). Type in the file name of your phylip formatted file.

PHYLIP dnadist Steps

#PHYLIPdnadistExecutionStep

4. A Menu-Style to indicate parameters will pop. If you are satisfied with the parameters, click Y and enter. If the program is DONE. Quit.

PHYLIP dnadist Steps

#PHYLIPdnadistAnalysisStep

5. Open outfile. And you will see the results of the distances between species.

6. Rename outfile to infile for the next function.

PHYLIP neighbor Steps

#PHYLIPneighborAnalysisStep

5. Open outfile. And you will see the results of the distances between species.

6. Rename outfile to infile for the next function.

Classmate: ah so I computed for their distance difference. And so? After that? What if I want to visualize the, you know, TREE? The puno of it all! Cheline: oh. Thats easy too! Just click on the neighbor exe file why you so conyo?!

PHYLIP neighbor Steps

#PHYLIPneighborAnalysisStep

1. Make sure you rename outfile to infile . 2. Click on the neighbor exe file. If you are satisfied with the parameters, go click Y and enter.

PHYLIP neighbor Steps

#PHYLIPneighborAnalysisStep

3. Open the outtree file.

4. Open the outfile. And you will see a TREE! and the resulting distances between nodes.

Classmate: oh Rachelle! It is so awesome! But why doesnt it look like the other trees I have seen before? Its so lame to view in the notepad! Cheline: Easy, girl/boy/bakla/tomboy/butiki/baboy! Patience is a virtue.

PHYLIP drawgram Steps

#PHYLIPdrawgramAnalysisStep

1. 2. 3. 4.

Make sure you rename outtree to intree. AGAIN. Click on the drawgram exe file. Type a font. (e.g., Font1-Font6) If you are satisfied with the parameters, go click Y and enter.

Classmate: Darling, thank you, thank you I get it now! I can easily identify the groups and the clade and the root! you go girl! Cheline: OH PLEASE. Now, pay me! :P Joke. ACTUALLY, THE SAME PROCESS IS TRUE FOR prodist. for protein sequences.

THY WORKSHOP
#PHYLIPworkshop Using the dnadist exe file, show a phylogenetic tree of the DNA sequence of 6 species. Follow-up questions: 1. How many branches are there? 2. How many nodes? 3. Give an example for each group. 4. Give an example of a homologue and a paralogue.
6 447 Human Bovine CAGACGAGAT GCAGCGACTA TGTGTGTATG TGCTGATCTT TGCACTGGCT CTGGCCGCCT TCTCTGAAGC TTCTTGGAAG CCCCGCTCCC AGCAGCCAGA TGCACCCTTA GGTACAGGGG CCAACAGGGA CCTGGAGCTA CCCTGGCTGG AGCAGCAGGG CCCAGCCTCT CATCATCGAA GGCAGCTGGG ACCCCAGGGT CCCCCACACC TCGTGGCAGA CCCGTCCAAG AAGCAGGGAC CATGGCTGGA GGAAGAAGAA GAAGCCTATG GATGGATGGA CTTCGGCCGC CGCAGTGCTG AGGATGAGAA CTAACAATCC TAGAACCAAG CTTCAGAGCC TAGCCACCTC CCACCCCACT TCAGCCCTGT CCCCTGAAAA ACTGATCAAA AATAAACTAG TTTCCAGTGG ATC------- ---------- ---------- ------CAGGCTCCAG GCCAACAGCA GCGTCACCCA CCTCCCAGCT TCACAGACAA GATGCAGCGA CTGTGTGCAC ATGTGCTGAT CTTGGTGCTG GCTCTGGCCG CCTTCTGCGA AGCTTCTTGG AAGCCCCACT CCCACCTGCA AGACGCGCCC GTCGCTCCAG GGGCCAATAG GGGCCAGGAG CCGCTCAGGA TGAACCGGCT GGGCCCAGCC TCGAACCCCC GGAGGCAGCT GGGGCTTCAG GATCCGCCAC ACATGGTCGC AGACCTGTCC AAGAAGCAGG GGCCATGGGT GGAGGAAGAG GAAGCAGCAT ATGGATGGAT GGACTTCGGC CGCCGCAGTG CTGAGGAAGG GGACCAACAT CCCTGAGAAC AAGCTTTGGA GCCCAGTCAC CTCCCAGCCC AGCCCAGCCC CATGAAACAC ACATCAAAAT AAACTAGCTT CCAATGG CCATCCGCAG CTTCTCCCAC GTCCCATCTC TGCAGACAAG ATGCGGCGAC TGTGTGTGTA TGTGCTGATC TTTGCGCTGG CTCTGGCCGC CTTCTCCGAA GCTTCTTGGA AGCCCTGCTC CCAGCTGCAG GACGCACCCT CAGGTCCAGG GGCCAATAAG GGCCTGTACC CGCATTGGCC AGACCAGCTG GACAGGCTGG GCCCAGCCTC TCATCACCGA AGGCAGCTGG GGCTCCAGGG TTCCCCACAC TTGGTAGCAG ACCTGTCCAA GAAGCAAGGG CCATGGCTGG AAAAAGAAGA AGCAGCCTAC GGATGGATGG ACTTTGGCCG CCGCAGCGCT GAGGAAGGGG ATCAAAGTCC TTAGAAAAAG CTTGGGAGCC CAGCCGGCTC CCACCCAGCC CAGCCCTGCC CTGTGAAAAA CCAACCAAAA TAAACTAGCT TCGGATG AAAGTGCGGA CGGAGCGCAG GGAGAGGTGC GGAGCCCCCG GAGCAGCAGC GTGAGCCATG AAGACGAAGG TGTTCCTCGG CCTCATCCTC AGCGCGGCGG TGACCGCCTG TCTGTGCCGG CCGGCAGCGA AGGCCCCGGG GGGCTCCCAC CGCCCCACCT CCAGCCTGGC CCGGCGGGAT TGGCCCGAGC CCCCGTCCCA GGAGCAGCAG CAGCGCTTCA TCTCCCGCTT CCTGCCCCAC GTCTTCGCAG AGCTGAGCGA CCGCAAAGGC TTCGTGCAGG GGAACGGGGC GGTAGAGGCC CTGCACGACC ACTTCTACCC CGACTGGATG GACTTCGGCC GCCGGAGCAC AGAGGATGCG GCCGATGCCG CGTAGCCCGC GCAGCGCCCC GACCCTCTCA GCACATCTCT GGTCCCGCAA TAAAGCTTTG GCACTCCC-- ------AGAGCAGAGC TGACCCAGCG CCACAACAGC CAACTATTCC CCAGCTCTGT GGACAAGATG CCTCGACTGT GTGTGTACAT GCTGGTCTTA GTGCTGGCTC TAGCTACCTT CTCGGAAGCT TCTTGGAAGC CCCGCTCCCA GCTACAGGAT GCATCATCTG GACCAGGGAC CAATGAGGAC CTGGAACAGC GCCAGTTCAA CAAGCTGGGC TCAGCCTCTC ACCATCGAAG GCAGCTGGGG CTCCAGGGTC CTCAACACTT CATAGCAGAC CTGTCCAAGA AGCAGAGGCC ACGGATGGAG GAAGAAGAAG AGGCCTACGG ATGGATGGAC TTTGGCCGCC GCAGTGCTGA GGAAGACCAG TAGGACTAGC AACACTCTTC CAGAGCCCAG CCATCTCCAG CCACCCCTCC CCCAGCTCCG TCCTTACAAA ACATATTAAA AATAAGC TCCAGGCTCT GAAGGATCAC TGCAACAGAA ATGGACAAGA AGGTTTGTGT TAGTATTCTG CTAGCCATGC TTGCCATAGC AGCCTTGTGC AGGCCAATGA CAGAGCTAGA ATCAGCAAGA CACGGAGCTC AAAGGAAGAA CTCCATTTCT GATGTCAGCA GACGGGACCT CCTAGCATCC CTGACCCATG AACAGAAGCA GCTGATCATG TCACAGCTTC TCCCCGAGCT ACTTTCAGAA CTCTCCAATG CTGAGGACCA TCTTCACCCC ATGCGTGACC GGGACTATGC TGGATGGATG GATTTTGGCC GCAGAAGTTC TGAAGTCACA GAATCTTAAA TCCTTTCCTT TACCATCTCT GCCTATTTTA CTGCTGTGAA CGTCCCAATG GGGATTAATG ATGCTAATAA ATTATTGGTC TGAT------ ---------- -------

Horse

Chicken

Mouse

Rat

THY WORKSHOP
#PHYLIPworkshop
10 124 Buffalo

Using the prodist exe file, show a phylogenetic tree of the DNA sequence of 6 species. Follow-up questions: 1. How many branches are there? 2. How many nodes? 3. Give an example for each group. 4. Give an example of a homologue and a paralogue.

KETAAAKFQR QHMDSSTSSA SSSNYCNQMM KSRNMTSDRC KPVNTFVHES LADVQAVCSQ ENVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHY DASV Giraffe KESAAAKFER QHIDSSTSSV SSSNYCNQMM TSRNLTQDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSAMS ITDCRETGNS KYPNCAYQTT QAEKHIIVAC EGNPYVPVHY DASV Goat KESAAAKFER QHMDSSTSSA SSSNYCBZMM KSRNLTQDRC KPVNTFVHES LADVZAVCSZ KNVACKNGZT BCYQSYSTMS ITBCRZTGSS KYPNCAYKTT QAEKHIIVAC ZGBPYVPVHF DASV guinea pig AESSAMKFER QHVDSGGSSS SNANYCNEMM KKREMTKDRC KPVNTFVHEP LAEVQAVCSQ RNVSCKNGQT NCYQSYSSMH ITECRLTSGS KFPNCSYRTS QAQKSIIVAC EGKPYVPVHF DNSV hippopotamus KETAAEKFQR QHMDTSSSLS NDSNYCNQMM VRRNMTQDRC KPVNTFVHES EADVKAVCSQ KNVTCKNGQT NCYQSNSTMH ITDCRETGSS KYPNCAYKTS QLQKHIIVAC EGDPYVPVHY DASV muskrat KETSAQKFER QHMDSTGSSS SSPTYCNQMM KRREMTQGYC KPVNTFVHEP LADVQAVCSQ ENVTCKNGNS NCYKSRSALH ITDCRLKGNS KYPNCDYQTS QLQKQVIVAC EGSPFVPVHF DASV pig KESPAKKFQR QHMDPDSSSS NSSNYCNLMM SRRNMTQGRC KPVNTFVHES LADVQAVCSQ INVNCKNGQT NCYQSNSTMH ITDCRQTGSS KYPNCAYKAS QEQKHIIVAC EGNPPVPVHF DASV pronghorn KETAAAKFER QHIDSNPSSV SSSNYCNQMM KSRNLTQGRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QAKKHIIVAC EGNPYVPVHY DASV sheep KESAAAKFER QHMDSSTSSA SSSNYCNQMM KSRNLTQDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QAEKHIIVAC EGNPYVPVHF DASV whale RESPAMKFQR QHMDSGNSPG NNPNYCNQMM MRRKMTQGRC KPVNTFVHES LEDVKAVCSQ KNVLCKNGRT NCYESNSTMH ITDCRQTGSS KYPNCAYKTS QKEKHIIVAC EGNPYVPVHF DNSV