1.ADD TO INTRO-What are we trying to accomplish and create through DNA barcoding? DNA barcoding is just a tool we’re using for a larger purpose. How will our research contribute to science and conservation?
2. Build a phylogenetic tree- based on the data. Please use this as a road map to complete assignment 3.
You can download MEGA X for free by following this link: https://www.megasoftware.net/
bee samples attached-
Extra info for the tree
- You cannot build a MEGA phylogenetic tree out of sequences acquired by different primers. These primers cause different genes to be copied in PCR, so they produce different sequences. MEGA builds a phylogenetic tree by comparing sequences, so adding different sequences from the same specimen would produce a tree telling you that the same specimen is two different species. So you may want to make 2 phylogenetic trees – one for each primer. Comparing the species ID and phylogenetic trees for each primer would be a really interesting discussion topic.
- In the interest of creating neat phylogenetic trees, I have attached an excel file with fewer sequences, because there’s no point in creating a phylogenetic tree with several sequences from the same subspecies unless they’re from different locations.
- Some kind of table or graph showing bee species (don’t do all of these, just pick 1 or 2 depending on what you would like to show)
- Add species/subspecies to your pre-existing table that shows concentration and purity (for both primers because different primers give different results)
- Or could make a separate table just showing the different species at each site (still use both primers though)
- Could make a graph showing the frequency of each subspecies so we can see which are most common
- Interpret your results
- Which species were common or rare? Were there differences between locations or hives?
- Differences between primers?
- Did one primer tend to produce more bands on the gel?
- Did one primer produce a different subspecies after sequencing?
- How does this specifically relate to the larger picture of science and conservation?
- Future research directions
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