Evolution-Phylogeny Activity (updated 1/2014)



  1. View: HHMI Click and Learn on: Sorting Seashells

  2. View: HHMI Click and Learn on: Species Relationships Based on Sequence Similarity



Constructing Phylogenetic Analyses:

There are a variety of ways to accomplish this task using a variety of tools and platform (programs). You will need to practice before you pick your personal inquiry activity. (see below all the project suggestions)

Here are some examples and ideas to pursue, feel free to pick and choose your own ideas:

(NOTE: some of the activities ask for a distance matrix Surprisingly, and unfortunately, phylogeny.fr does not appear to support this option for clustalw. However, Mobyle does support this for clustalO. If you enter a name for output distance matrix and the output tree. http://mobyle.genouest.org/cgi-bin/Mobyle/portal.py#forms::clustalO-multialign It will print the tree and distance matrix for you. Information from Mark Miller at SDSC).



  1. Comparing DNA Sequences on Mollusks (this activity requires downloading of 2 programs to complete. http://www.clustal.org/clustal2/ and http://pbil.univ-lyon1.fr/software/njplot.html and sequence files http://media.hhmi.org/biointeractive/activities/shells/molluscDNAfiles.zip

  2. Traditional College Board AP Lab: CB New Investigation #3 DNA Blast
    PPT and other information Gene 1, Gene 2, Gene 3, Gene 4 (files need to be saved to your computer first for upload into BLAST) (Accession #s are 1) AF137273 2)BT050432.1 3)XM_002188156.2 4)AF511507.1 if you don't have a computer you can save files on).

  3. Plasmodium Phylogeny Project: short video; fecal sample sequences; how to build a tree Suggested project -Look at the Plasmodium sequence data summary and site map from the Liu et al. (2011) study and generate a list of observations and questions. Select the Plasmodium sequences from 2 collection sites and run a multiple sequence alignment to get a sense of how similar/different the parasites are from each other. Creating a distance tree will help to determine if the sites have independent or mixed Plasmodium populations.

  4. Blast Human vs Chimp DNA- using HBB (note: you might want to use the http://www.phylogeny.fr/ site see podcast from Mr. Knuffke on an example of how to do the project using phylogeny.fr)

  5.  Primate Activity (alternate Primate activity) (note the NGWB site lost it's funding and is no longer in existence, you can use the one click on the http://www.phylogeny.fr/ site to do essentially the same activities, however avoid using an underscore “_” in modifying the organism name- that can cause problems). Be sure to watch a podcast from Mr. Knuffke on an example of how to do the project using phylogeny.fr).

  6. Walruses, Whales, Seals (note the NGWB site lost it's funding and is no longer in existence, you can use the one click on the http://www.phylogeny.fr/ site to do essentially the same activities, however avoid using an underscore “_” in modifying the organism name- that can cause problems). Be sure to watch a podcast from Mr. Knuffke on an example of how to do the project using phylogeny.fr). UPDATE: here are some updated instructions if you want to try this with MEGA (see #10 below): Whale MEGA Instructions (let me know if there are any corrections that need to be made).

  7. Bears and Pandas ((note the NGWB site lost it's funding and is no longer in existence, you can use the one click on the http://www.phylogeny.fr/ site to do essentially the same activities, however avoid using an underscore “_” in modifying the organism name- that can cause problems). Be sure to watch a podcast from Mr. Knuffke on an example of how to do the project using phylogeny.fr).

  8. Go to JGI (Joint Genome Institute) Genome Portal (located in Walnut Creek, CA). There is also a Fungal Genome Portal and a Plant Genome Portal. You can download tons of new genomes to look at and compare. You will need to register for a free account to access the data.

  9. Activity from Bioinformatics Activity Bank: Link to background PPT Medical Problem Solving of Seizures OR Medical Problem Solving Anemia with Microarray Data

  10. For the really adventurous (you know who you are!), download MEGA (for MAC or PC). Here's the MEGA tutorial.

  11. Just in case this list isn't exciting enough here is a link to a site with all “known” platforms



Phylogeny Lab Part 2 Experimental Planner (adapted and borrowed almost exactly and completely from David Knuffke) (podcast from Mr. Knuffke on an example of how to do the project using phylogeny.fr)

Answer the following questions as best you can to have a successful data-gathering experience for part 2 of your Phylogeny Lab.

  1. What is the phylogenetic question that you are interested in investigating (note: the more specific your answer is to this question, the better off the rest of this is going to go).

  1. What gene/genes are you going to analyze?

  1. What is the shorthand code for the gene/genes you are going to look at?

  1. Why are you going to look at the gene/genes that you have chosen to look at?

  1. Are you going to analyze DNA sequences or protein sequences?

  1. Where are you going to get your sequences from?

  1. What organisms are you going to get sequences from for your analysis?

  1. What are their scientific names?

  1. Why are you going to look at these organisms?

  1. What will be the outgroup organism that you use?

  1. What website(s), if any, will you use to carry out your analysis?

  1. What program(s), if any, will you use to carry out your analysis?

  1. What steps will you run to carry out your analysis?

  1. Where will you go to do some research to see if what your tree tells you jives with current phylogenetic understanding from the research community?

  1. Are you happy with your answers to all of the above questions? If not, which ones do you want direct teacher assistance?

That’s it. Now just do what you wrote you were going to do, make your presentation (or write your article, or your report, or whatever I’m having you do), and post it on the class blog http://grochapbiology.blogspot.com/. You’re done! (example projects: http://breakingbio.blogspot.com/ )



Phylogenetic Analysis Article Guidelines

Overview:

For the past little while, you have been trained on using a variety of “industry standard” websites and programs to investigate the evolutionary relationships between different organisms via analysis of similarities and differences in DNA and protein sequences.  It’s been fun.  Now that you are certified, you will be applying your new bag of tricks to investigate the evolutionary relationships among a group of organisms of your own choosing.  You will compose a scientific article describing the results of your investigation, which you will publish to the course blog http://grochapbiology.blogspot.com/.  Essentially the question you are trying to answer is:



How are <insert organism(s) here> related to <insert organism(s) here>?

To answer this question, you are going to have to make a series of decisions, collect a good amount of appropriate sequence data, and then analyze that data.

The article that you create will be evaluated according to the following rubric: (for a general description of what excellence looks like go to: http://www.grochbiology.org/AdaptedGeneric_Lab_Rubric2013.htm)



Category: (points)

Criteria:

Introduction: (1-4)

  • The introduction has a properly stated version of the question you are addressing.

  • The introduction provides some information as to why this question is interesting.



Methods: (1-4)

  • Your choice of sequence data is stated and the validity of its usage is explained.

  • The analytical process you used is described.



Results: (1-4)x2

  • At least one tree diagram generated during your analysis is presented.

  • The relationships indicated in this tree diagram (and any additional tree diagrams) are described fully.

  • If your question is most appropriately addressed through the generation and description of multiple tree diagrams, this is done.



Discussion: (1-4)x3

  • The results of your analysis are compared to primary/professional source literature (articles, reputable websites, textbooks).

  • Any discrepancies or alignment between your results and the professional literature are discussed, and justified on sound scientific grounds.

  • At least two additional sources of evidence that could be considered in addition to the evidence you used are discussed, and justified on sound scientific grounds.



References (1-4)

  • The article contains at least two references to professional literature.

  • Any websites or programs that are used in the analysis are included in the articles as hyperlinks (hyperlink to the website where the program lives if you use programs).

  • The data sources that are used in the analysis are referenced, with hyperlinks.

  • All references to professional literature are included at the end of the article and cited in-text in the APA format.



Aesthetics:  (1-4)

  • The article is properly structured.

  • The article uses appropriate language that is not needlessly simplistic or overly complex.

  • The article has no noticeable grammatical, syntactical, or spelling errors.



Length: (1-4)

  • The article is at least 750 words in length (for reference, this document is 550 words in length).

  • The article is long enough to thoroughly address the requirements of the project, but not so long as to be needlessly boring.



Posting: (1-4)

  • The article is posted to the blog on time.

  • The article is posted as either the body of a post, or as an embedded (not linked) google doc, according to the instructions demonstrated on this video:  http://goo.gl/YKKbQ

  • The article’s post has the lables “article”, “phylogeny”, and any others that you feel are appropriate



Readership (1-4)

  • You have left two comments on two other posts that indicate that you have read the articles, and that offer constructive feedback or informed questions.

  • You have responded to all comments on your own article in a timely fashion (within 24 hours).