Generation of Phylogenetic Tree based upon DNA sequence analysis
Generation of Phylogenetic Tree based upon DNA sequence analysis is a lab exercise created by Scott Cooper, Associate Professor of Biology at University of Wisconsin at La Crosse. Cosmetic alterations only were made by Nigel Goldenfeld.
There are two steps to creating a phylogenetic tree:1. Aligning the DNA sequences
2. Using the aligned DNA sequences to generate a tree
First we will align DNA sequences from the Mitochondrial D-loop from five species (Human, Chimp, Gorilla, Orangutan and Neanderthal). These sequences can be found at the site Primates . They have also been pasted below.
Log onto the Biology WorkBench, select Session Tools and create a new session named phylo.
Select Nucleic Tools and then scroll down to Add New Sequence.
Create files for each species and paste in the mitochondrial D-loop sequence.
Select the sequences that you wish to align by clicking the box next to each file, and then select CLUSTALW.
You will now be given some options on parameters you can change in your alignment. You can just use the default values and select Submit at the bottom of the page.
Select Import Alignment(s). This will save this alignment in a single file for further analysis.
Next select Alignment Tools select the aligned sequences by clicking the box next to the file name.
Next click either the button DRAWTREE or DRAWGRAM.
DRAWTREE draws a rooted tree.
DRAWGRAM draws an unrooted tree.
You will now be given some options on parameters you can change in your alignment. You can just use the default values and select Submit at the bottom of the page.
The tree will now appear.
Congratulations you are now an evolutionary biologist.
Which species appear to be the most closely related?
From your tree, does it appear that Neanderthals were direct ancestors of humans, or did we share a common ancestor that branched off from the other apes?
Example D-loop hypervariable regions from five primate species.
>gi|2286205|gb|AF011222.1| Homo
sapiens neanderthalensis mitochondrial D-loop hypervariable region 1
GTTCTTTCATGGGGGAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAGCAACCGCTATGTATCTCGTACATTACTGTTAGTTACCATGAATATTGTACAGTACC
ATAATTACTTGACTACCTGCAGTACATAAAAACCTAATCCACATCAAACCCCCCCCCCCATGCTTACAAGCAAGCACAGCAATCAACCTTCAACTGTCATACATCAACTACA
ACTCCAAAGACGCCCTTACACCCACTAGGATATCAACAAACCTACCCACCCTTGACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTACAGTCAAATCCCTT
CTCGCCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAT
>neanderthal_2000
CCAAGTATTGACTCACCCATCAACAACCGCCATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACCATAATTACTTGACTACCTGTAATACATAAAAAC
CTAATCCACATCAACCCCCCCCCCCCATGCTTACAAGCAAGCACAGCAATCAACCTTCAACTGTCATACATCAACTACAACTCCAAAGACACCCTTACACCCACTAGGATAT
CAACAAACCTACCCACCCTTGACAGTACATAGCACATAAAGTCATTTACCGTACATAGCACATTATAGTCAAATCCCTTCTCGCCCCCATGGATGACCCCCCTCAGATAGGG
GTCCCTTGA
>gi|975204|emb|X90314.1|MTHSWGICB H.sapiens mitochondrial DNA for D-loop (isolate
WG+ice37+B)
TTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTTACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGCACGGTACCA
TAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAA
CTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCT
CGTCCCCATGGATGACCCCCCTCA
>gi|3766221|gb|AF089820.1|AF089820 Gorilla gorilla beringei mitochondrial D-loop,
partial sequence
TTCTTTCATGGGGAGACGAATTTGGGTGCCACCCAAGTATTAGTTAACCCACCAATAATTGTCATGTATGTCGTGCATTACTGCCAGCCACCATGAATAATGTACAGTACCA
CAAACACTCCCCCACCTATAATACATTACCCCCCCTCACCCCCCATTCCCTGCTCACCCCAACGGCATACCAACCAACCTATCCCCTCACAAAAGTACATAATACATAAAAT
CATTTACCGTCCATAGTACATTCCAGTTAAACCATCCTCGCCCCCACGGATGCCCCCCTTCAGATAGGGATCCCTTAAACACCATCCTCCGTGAAATCAATATCCCGCACAA
GAGTGCTACTCTCCTCGCTCCGGGCCCATAACACCTGG
>gi|6288860|gb|AF176766.1|AF176766 Pan troglodytes troglodytes isolate DODO
mitochondrial D-loop, partial sequence
GTACCACCTAAGTATTGGCCTATTCATTACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACAGTACTATAACCACTCAACTACCTATAATACAT
TAAGCCCACCCCCACATTACAACCTCCACCCTATGCTTACAAGCACGCACAACAATCAACCCCCAACTGTCACACATAAAATGCAACTCCAAAGACACCCCTCTCCCACCCC
GATACCAACAAACCTATGCCCTTTTAACAGTACATAGTACATACAGCCGTACATCGCACATAGCACATTACAGTCAAATCCATCCTTGCCCCCACGGATGCCCCCCCTCAGA
TAGG
>gi|1743293|emb|X97708.1|MIPACONTR P.abelii (YN91-227) mitochondrial DNA for control
region
TTCTTTCATGGGGGACCAGATTTGGGTGCCACCCCAGTACTGACCCATTTCTAACGGCCTATGTATTTCGTACATTCCTGCTAGCCAACATGAATATCACCCAACACAACAA
TCGCTTAACCAACTATAATGCATACAAAACTCCAACCACACTCGACCTCCACACCCCGCTTACAAGCAAGTACCCCCCCATGCCCCCCCACCCAAACACATACACCGATCTC
TCCACATAACCCCTCAACCCCCAGCATATCAACAGACCAAACAAACCTTAAAGTACATAGCACATACTATCCTAACCGCACATAGCACATCCCGTTAAAACCCTGCTCATCC
CCACGGATGCCCCCCCTCAGTTAGTAATCCCTTACTCACCATCCTCCG