This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is phylogenetics?
Phylogeny is a way of tracing ancestry of species. Branches or organisms diverge at speciation events [1]. Speciation events are moments in evolutionary time when an event gives rise to a new species [2]. Phylogenetics allows us to trace the common ancestry of species. Two species are more related if they share a more recent common ancestor and are less related if they share a less recent common ancestor [3].
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Different ways of analyzing phyologeny
Maximum Likelihood
Identifies a tree that maximizes the probability of the genetic data given the tree.
Neighbor-Joining
This method makes quick trees but is not very reliable. They are good for giving an idea of what the tree should be.
Average Distance
This method assumes that species equally diverged from a common ancestor. It uses similarity scores to identify closely related species and joins them with equal branch length.
How to construct Phylogeny trees
The first step in creating a phylogenetic tree is to compile FASTA sequences for protein sequence from organisms of interest. This can be done by searching on NCBI. The next step is to use MEGA to align these FASTA sequences (shown in Figure 3). When the sequences are aligned, MEGA can create different phylogenetic trees depending on the preferred method.
Step 1. Compile protein sequences in a FASTA file.
I need to figure out how to upload FASTA file
Step 2. Align FASTA sequences
Step 3. Construct Phylogenetic tree.
References
[Header Image] http://www.oceanographerschoice.com/log/wp-content/Evo_large.gif
[1] (n.d.). Retrieved March 14, 2018, from https://evolution.berkeley.edu/evolibrary/article/evo_05
[2] Speciation event. (n.d.). Retrieved March 14, 2018, from https://www.biology-online.org/dictionary/Speciation_event
[3] Phylogenetic trees. (n.d.). Retrieved March 15, 2018, from https://www.khanacademy.org/science/biology/her/tree-of-life/a/phylogenetic-trees
[1] (n.d.). Retrieved March 14, 2018, from https://evolution.berkeley.edu/evolibrary/article/evo_05
[2] Speciation event. (n.d.). Retrieved March 14, 2018, from https://www.biology-online.org/dictionary/Speciation_event
[3] Phylogenetic trees. (n.d.). Retrieved March 15, 2018, from https://www.khanacademy.org/science/biology/her/tree-of-life/a/phylogenetic-trees