Article for Amanda and Morgan’s presentation on October 26th
Exam #2 on Monday, October 29th
Practice data matrix for tree building
Reading/Listening assignments

For Fri Oct 26
Take notes on these thought questions about Amanda and Morgan’s paper on toxin resistance in garter snakes:

  1. What is the significance of adding the Illinois population as an outgroup in Figure 1?
  2. What model organism was used in the experiment to test sodium channel function?
  3. What are the physical effects to garter snakes when exposed to tetrodotoxin (TTX)?
  4. What is Kd measuring in this study? How is measuring Kd similar to Km?
  5. One way garter snakes could evolve resistance to TTX is by altering the proteins that this toxin binds to. What do the authors argue is a second way that these snakes could evolve resistance? Which method of adaptation is used by the snakes?

For Wed Oct 24
We will look at the alpha crystallin thermal adaptation paper that we did not get to on Friday.
We will also review material for the exam - come to class with your questions about anything covered so far.
We shouldn’t finish this section of the course without reading some of Darwin’s own writing. Read the end of the last chapter of Darwin’s
On The Origin of Species (the last 17 paragraphs starting with “The fact, as we have seen, that all past and present . . .”).

For Fri Oct 19th
We will use this paper to discuss another way that the comparative approach has been used to examine molecular adaptation to environmental temperature. This paper does not examine enzyme function, but the ability of proteins called molecular chaperones to prevent other proteins from clumping together (aggregating) when under stress (high temperatures, osmotic stress, etc.). We will use this paper to:
  • Examine the data that shows correlations between a species’ environmental temperature and the stability and chaperone/protective function of its aA-crystallin protein (figure 2 and 3A)
  • How a computer algorithm called TreeSAAP was used to identify aA-crystallin regions where natural selection has changed the level of hydrophobicity (figure 3D)
  • Identification of a single amino acid substitution altering hydrophobicity that changes both protein stability and protective function (figure 5 and 6)

You will need to submit on Angel a write-up of the phylogenies you have constructed using Phylogeny.fr. Your write-up should contain the following:
  • A table listing the gene name(s), species and accession numbers for the sequences in your analysis
  • Three phylogenetic trees as follows
    • Two phylogenies using the same nucleotide sequences but with different tree construction methods
    • A third tree constructed from the amino acid translations of each of your gene’s coding sequences
  • A narrative that introduces the gene of study, provides the methods used to construct each of your trees and discusses the quality of the trees produced. You should also discuss whether there were any differences in topology (branching) between your three trees, and what this means.

For Wed Oct 17
We will discuss the data and conclusions from Dong and Somero 2009
  1. Km values are a measure of enzyme activity. According to figures 1 and 2, what is the relationship between thermal environment and Km value? How does this figure show that cMDH from each species may be adapted to different thermal environments? You can ignore the insets in these figures.
  2. What does figure 3 add to this paper?
  3. cMDH in L. digitalis and L. austrodigitalis differs by only one amino acid. What do the authors argue is the functional effect of this difference?

For Mon Oct 15
We will finish any thought questions on the Hochachka reading we do not get to on Friday.
We will then discuss a great example of comparative physiology/biochemistry, the thermal adaptation of cytosolic malate dehydrogenase (cMDH) reported by
Dong and Somero 2009. Be ready to discuss these questions about the introduction of the paper:
  1. What is the rationale for this study?
  2. Why do intertidal organisms along the Pacific coast of North America make good study systems for studying thermal adaptation?
  3. What are the benefits of using the limpet genus Lottia for studying thermal adaptation? What is especially significant about studying thermal adaptation in L. digitalis and L. austrodigitalis? Why is it important to the study that the species used are closely related to each other?
  4. Why do the authors focus on the single protein cMDH? What aspects of this protein do the authors use to monitor its possible adaptation to different temperatures?

For Fri Oct 12th
We will look at the example phylogenetic trees you found for class.
Read pages 3-13 from
Chapter 1 of Hochachka and Somero’s Biochemical Adaptation. Take notes on the following questions and be ready to talk about them in class. Submit answers to the first five questions using the content tab of Angel.
  1. What are some of the challenges to “dissecting out” a biochemical system to study?
  2. What is your concept of an adaptation coming into this class?
  3. What do Gould, Lewontin and Vrba mean when they break adaptation into two components – “process” and “current utility”? How does the example of glycerol as an anti-freeze molecule highlight the importance of understanding the evolutionary history of a biochemical trait?
  4. What is the difference between the terms adaptation, exaptation and aptation?
  5. In what sense is the evolution of using glycerol to achieve freezing resistance an exaptation, and in what sense is it an adaptation? (hint: use the discussion on page 8 to discern the difference between the inherent properties of the glycerol molecule, and the way that it interacts with metabolic pathways).
  6. What is “comparative physiology” and what are its strengths? Why should someone with an interest in human or mammalian physiology spend time studying invertebrate physiology?
  7. Why does a comparative physiologist need to be concerned with the phylogeny of the species they are studying? What is the danger in interpreting “phylogenetic baggage” as adaptation?
  8. What contributions has molecular biology made to the study of comparative/evolutionary physiology?
  9. According to the first page of this chapter, why are biochemical systems particularly sensitive to environmental insult? What types of insult does the environment dish out?

For Wed Oct 10th
  • Read pages 57-60 in this section from Phylogenetic Trees Made Easy. These pages describe the different approaches for estimating phylogenetic trees.
  • Review the Thewissen paper and take notes on what method was used to produce its phylogeny.
  • Bring in a hard copy (or email to me an electronic copy prior to class) of one phylogenetic tree you find in the scientific literature. Be ready to explain to the class what type of method was used to make the tree. You only need a copy of the first page of the paper and the figure with the tree. Feel free to use either a species/taxon phylogeny or gene phylogeny.

For Mon Oct 8th
Bring your laptop to class along with a file containing eight gene sequences from your assigned gene family.

For Fri Oct 5th
We will finish discussion of the Thewissen paper
Read
this web page on using phylogenetic trees for classification
Download
the free phylogenetic software Mega to your laptop and bring it to class with you

For Wed Oct 3rd
We will be discussing this paper on whale evolution by Hans Thewissen from the NEOMED in Kent. Be ready to discuss the following questions in class:
  1. What are the biogeographical and temporal problems with the hypothesis that Cetaceans and Hippopotamus are sister taxa?
  2. How are these problems solved with the revised hypothesis that the family Raoellidae is the sister taxon to Cetaceans?
  3. What synapomorphies support this later hypothesis?
  4. The authors present two possible ways to classify the order Cetacea.  Which makes more sense to you?
  5. How do the authors characterize the niche of Indohyus?  How do the fossil remains support this conclusion?  How does this conclusion change the concept of early Cetacean evolution?

For Mon Oct 1st
Here is a detailed chapter on phylogenetic trees and tree construction that we will work with on Monday. Read pages 11-22 and 28-31. You can ignore the section on “Splits”. Some questions to think about:
  1. What is a polytomy?
  2. What is the distinction between a phylogeny and cladogram?
  3. What is homoplasy, and what types of homoplasy can occur?
  4. What is the difference between monophyletic, paraphyletic and polyphyletic groups? Which type should be used to name taxa when creating classification systems? Why?

For Fri Sep 28th

Read
this chapter from Edward Larson’s book Evolution for Friday and take notes on the following thought questions:
  • What are the key features of catastrophism, progressivism and idealism? Which scientists were adherents to each of these philosophies, and which agreed with the concepts of evolution and which disagreed?
  • Why does a Lamarckian view of life conflict with the concept of species? Be ready to discuss what is meant by the term species.
  • How did catastrophists explain the increasing amounts of organismal change being discovered in the fossil record throughout the early 1800’s?
  • Shared features between a group of taxa, such as similar bones in the limbs of all land vertebrates, was used by Darwin as one of the primary lines of evidence for evolution. What was Richard Owen’s non-evolutionary interpretation for these observations?

For Wed Sep 26th
Read the following sections of the Phylogenetic Systematics site from UC Berkeley
  • How to read an evolutionary tree
  • How to reconstruct an evolutionary tree
Pay special attention to hyperlinked terms on these pages. Be ready to discuss all of this content in Wednesday’s class.



Faculty and students in Fall 2009 traveled to a local talk by
evolutionary developmental biologist Dr. Sean Carroll
carrol