October 10

Oct. 3rd, 2018 Lab

This week in lab we used our fish DNA sample results to use Geneious and analyze the genomic data. None of my samples fostered adequate results (I think this was due to exposure to soy sauce and having to stay in my backpack for more hours than originally planned). Because of this issue, I used a sample that was sequenced prior, called NS01, NS02, and NS03.

NS01 was labeled as yellow tail, NS01 was halibut, and NS03 was bluefin tuna. To start out the analysis I was personally worried because I tend to struggle with computers and new software. I made myself slow down and follow each step of the handed out protocol and found it to be easier than expected. I was surprised with the ability of the site to perform the BLAST so quickly and utilize the NCBI data base within the same forum and at such a fast rate.

I faced a few bumps in the road outside of not being able to use my original data. I accidentally deleted my first sequence assembly as well as the folders with my reverse and forward transcripts, but luckily after having practiced with the software I was able to quickly re-download everything and start from scratch.


NS01 served as yellowtail

Top result from the BLAST:  Seriola quinqueradiata (Japanese amberjack-yellowtail) 


  1. BP: 445 (A instead of G)

There was only one polymorphism after deleting all of the ambiguities (N) with a hit start and hit end in the high thousands. Therefore my first sample was served as the correct fish.


NS02 served as Halibut

Top result from the BLAST: Paralichthys californicus voucher – California halibut


The reverse of the genomic data NS02 carried greater than 20 polymorphisms throughout the entire comparison whereas the forward and all other vouchers had no polymorphisms despite a 100% match.

  1. BP: 403 (T instead of C)

2.  BP: 413 (T instead of C)

3. BP: 418 (G instead of C)

4. BP: 421 (G instead of T)

5. BP: 428 (C instead of T)

6. BP: 435 (G instead of A)

7. BP: 438 (T instead of C)

8. BP: 442 (T instead of C)

9. BP: 443 (C instead of A)

10. BP: 458 (C instead of A)


NS03 served as Bluefin Tuna

Top result from the BLAST: Thunnus orientalis isolate – bluefin tuna

There were no polymorphisms present when comparing the matching sequences. With a 100% match and no polymorphisms it was surprising to see a slightly less than optimal hit start and end number below 1,000.

October 3

First Field Trip


I was sick during this field trip so I was unable to attend. The class went down the coast (south) to find  Lupinus arboreus for collection. We will be extracting DNA from these plants to better understand their genetics and population patterns.

October 3

Sept. 26th, 2018 Lab Field Trip

We took a lab field trip to see purple flowered lupine and Mimulus cardinals. We drove to Mt. Tamalpais followed by a trip to Stinson Beach and down the coast. Mount Tamalpais was supposed to have the red flowering Mimulus cardinals along wet water ways. Stinson Beach Coastal Cliffs are the environment of the purple flowered lupines.

Unfortunately, we were not able to find a flowering plant of Mimulus cardinals (we did find the plant, just not flowering). On the hike down to the water, it was noted that it would be extremely difficult for populations to share genomic information due to the sheer cliffs and hills. As the Mimulus cardinals is pollinated by humming birds, it is hard to imagine a humming bird being able to fly such long uphill distances between the different populations. This leads to geographic isolation that may seem small, but has a large effect on the Mimulus cardinals. We also discussed one of the oak tree family trees that was severely suffering from the fungal disease “sudden oak death.” The trees have very little genomic diversity leaving their population extremely susceptible to this disease. This is an issue with losing genetic diversity within a population because individuals do not have the possibility of diversity that may be needed to fight off pathogens.

On our search for the purple flowered lupine, we traveled closer to the coast near Stinson Beach. There were many plants in the area, but less flowers. As a self pollinating population, they appeared to be thriving even in the harsh winds of the coast line. The plant had almost soft looking leaves and a green color that was different from the other foliage present. In the areas of the lupine, many fennel plants were often present giving off their strong licorice smell. Mt. Tamalpais (looking for Mimulus cardinals)

Creek where populations of Mimulus cardinals would be found

Dr. Paul’s Secret Mimulus cardinals Plant along a small wet area

Drive from Mt. Tam to Coastal Area of the Purple Flowered Lupine

Environment of the Purple Flowered Lupine

The Purple Flowered Lupine Plant