Build a tree with your new sequence

If you have identified the sequence is from a bear, then it is possible to confirm this using a phylogenetic tree.

Select the "Bear Sequences" alignment and your "Consensus bear bile" sequence. Click Align/Assemble→Multiple Align and from the alignment options select "93% similarity", "global alignment with free end gaps" and "automatically determine sequences' direction" - then click OK.

You will notice that the DNA sequenced from the bear bile sample is shorter than the other sequences in the alignment - missing data such as this can influence how trees are constructed. In this exercise we are simply trying to find the genetic match to the Bear Bile sequence, not to accurately model bear evolution. Strictly speaking, we should "extract" the area of the alignment corresponding to the Bear Bile sequence and build a new tree (this is easy to do within Geneious - but is not a requirement of this tutorial).

Using this new alignment, build a tree by clicking the Tree button and using "HKY" as the Genetic distance model and "UPGMA" as the Tree building method. Select "Resample tree" using the bootstrap method, set to 100 samples and create a consensus tree.

Question 5: What is the closest relative to the DNA sequence isolate from the bear bile sample based on your phylogeny? (Note: Selenarctos thibetanus and Ursus thibetanus are the same species that has undergone a taxonic change).
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Question 6: Bootstrap values (or consensus support) on nodes give a measure of how stable the phylogentic tree is. Display the consensus support values on the tree (this can be located under the display options in the "Show node labels" menu. What is the % support that groups the bear bile sequence with its closest match on the tree?
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This concludes the Geneious "DNA forensics" tutorial. We hope you have found it useful. You can find answers to the questions here.