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BIOL 5130
Evolution
Phil
Ganter
301 Harned Hall
963-5782 |
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Salmon pens in the Bay of Fundy - What
sorts of adaptations might this new environment promote in domesticated
salmon? What
changes in the bay are possible? What effect might farming have
on wild salmon stocks?
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Assigments
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Assignment Schedule
Chapters
1 to 4 Assignment (s2)
- Define plesiomorphy
and apomorphy. Why is a synapomorphy useful in defining clades
while synplesiomorphies are not?
- The terms homology, homoplasy, and analogy
are confusing. Explain
the difference between them. Sequence
data is said to be more prone to some forms of homoplasy than is morphological
data. What sorts of homoplasy are more common in sequence data? Explain
why this is so.
- Without variation, there can be no evolution. Find an article in a juried
journal that measures genetic variation within a species or population(s) and
write a summary of the type of variation investigated, how it was measured,
and how much was found. Finally, discuss why this variation was of inteest
to the investigators and how evolution might have produced the variation or
how it might alter the variation in the future.
- Do either Option A or
B
- Option
A. There are many examples of evolution due to natural selection
in the literature. Find
an article in a juried journal that is an example and write a short summary
(one paragraph)
and an explanation of why it is a
good example of evolution due to natural selection.
- Option
B. Find
an article that looked for natural selection and failed
to find it and write a short summary (one paragraph)
and an explanation of why it failed to find evidence of
evolution due to natural selection.
Extra Credit: Find
an article that describes the origin of a new species (not one that describes
a new species) and present it to the class.
Chapter
5
The problem sheets will
be passed out in class
Chapters
6 and 7
- Genes are often split
into two types: housekeeping genes (those involved in basic cellular
processes like respiration, translation, etc.) and non-housekeeping (I couldn't
remember a better name, maybe environmental, but these are those genes that
code for proteins that are involved in an organisms interactions with its
environment). Discuss how these classes of genes might be viewed with
respect to natural selection, especially the expected dN/dS ratios from each
class.
- If heterozygotes are characteristic
of diploid organisms (polyploids too, I suppose), how can we speak of the
heterozygosity of a population of bacteria, all of whom are haploid? Second,
how do indels affect the measurement of heterozygosity (this may take some
searching on your part)?
- In the neutralist interpretation
of evolution the dN/dS ratio depends on the ratio of the neutral non-synonymous
mutation rate to the synonymous neutral mutation rate. How can there
be neutral non-synonymous mutations? What portion of synonymous mutations
should be neutral?
- When researchers core ice sheets and glaciers,
the cores are brought back to "core banks" and held at cold temperatures
for future research. One such line of research has been the attempt
to "revive" microbes from various levels in the cores (deeper levels
are older, sometimes tens of thousands of years older). How could such
research be used to check and calibrate a molecular clock?
- There are many examples
of attempts to measure natural selection at the sequence level in
the literature. Find an article in a juried journal that searches for
natural selection within a sequence and write a short summary (one paragraph),
an explanation of the method used to detect natural selection at a site in
a sequence, and a comment on their success and the relevence of the paper
to the discussion of selectionist versus neutralist views of evolution.
Remember, there are more methods for detecting selection than the dN/dS ratio
and any method will satisfy the requirements for this problem.
Crude
- Rather than do an assignment
on Chapters 8 and 9, I want to take a side-trip.
- The Australian
Broadcasting System has produced an interesting history of oil. Right,
petroleum. While
I am at the EPA, we will all take a foray into environmental science. There
are three parts to "Crude" and all three can be viewed at (you
can also google "crude ABC" and select the broadband
link:
- http://www.abc.net.au/science/crude/
- Roughly, the first part is a discussion of the
origins of oil (very surprising if you don't already know), the second
a look a how we use it and how much
we use and when we might run out, and the last part is a discussion of
the possible effects of our use of oil on the Earth's climate. By the way,
there are some audio issues in the first section, especially at the beginning,
but wait them out. Also, the site sometimes streams quickly and sometimes
can be slow. If it's too slow, try another time.
- What I want from you is this (keep a notebook open as you watch!):
- Where does oil come from according to this documentary (bonus points
if you can tell me what the Russians think!)
- What is the evidence for us nearing a peak in oil reserves?
- This is the centerpiece of this assignment. I
want you to:
- first, give me, in outline form, a synopsis
of the argument presented in the third segment about the effect
of our usage of oil on the
global climate. Be sure that the synopsis encompasses the entire
argument. You may have to watch the third segment more than
once to see this. ALSO be sure to view AN D INCLUDE the interviews
with Dr. Wallace Broecker and Dr. Lee Kump, as they add information
to the argument
- second, write a critique of the argument. Bonus
for finding evidence to support or weaken the scenario presented
I hope you find the show as fascinating as I
did. You may find all
of the interviews valuable and there is more on the formation of oil and
on peak oil if you click on the "web resources" link on the left
side of the page.
Chapters
10 & 11
This week we will take some time, as we have the
Spring Break, to work on the paper for the course. What each should do
is to investigate a topic of interest. Get some references, read them
and give me a title, paragraph describing the paper (the topic, why you chose
the topic, what the paper will cover, what questions you will raise and answer)
and a bibliography of sources you have at this point (expected to grow as you
do more research)
Chapter
12
- There are certainly
hemaphroditic animals but far fewer hermaphroditic animals than plants. This
brings up two questions:
- Why is hermaphroditism more common among plants
than animals?
- What is the distribution of hermaphroditism among
animals and does this distribution concur with the answer you gave in the
first question?
- What effect might variation in female choice have
on the outcome of Fisher's theory of runaway selection. If females
vary in thier degree of choice, say some will only mate with the male with
the longest tail while some will mate with males with shorter tails some
of the time, then what do you predict for the long-term change in male tail
length (give me as full of an argument, using digrams or numerical examples
if they help you make your point)?
- Find an article that is a test of either Zahavi's
or Fisher's hypothesis and write a summary of the article with a statement
of whether or not the hypothesis is supported and your opinon of the quality
of the work.
Chapters
13 & 14
Species are seen as individuals by some biologists.
In the class notes, they are contrasted with a piece of iron. The
species is an individual because it is bounded in time and space. The
iron is a class because it is not. But is that so? Consider whether
or not a piece of iron is bounded in space and time (must be both!) and whether
or not it can change.
The most important assignment is to work through
the Compleat Cladist
Chapter
5
We
Chapter
5
Chapter
5
Chapter
5
enrolled.
Chapter
5
Suppose
Chapter
5
It
Chapter
5
Now
Chapter
5
The
Chapter
5
It
Last Updated January 22, 2008