Take-Home Exam #2 (McCarthy)
1. Using ISI Web of Knowledge, I uncovered over
10,000 references (from the last 5 years) in the primary biological literature
using several keywords related to “ordination”.
Pick one paper that is closest to your area of biological interest that
utilizes ordination as the primary analytical tool. Provide a detailed
critique. More specifically, explain
what was done biologically, experimentally, and analytically. Detail what type
of ordination was done, resemblance coefficients used, interpretation made, etc. Were there better alternatives? Please provide me with a xerographic copy of
the paper when you submit your exam (I will return it). [20 points]
2. While collecting the overstory vegetation
data set previously provided in question #2 of Exam-1, we also collected a full
set of environmental data. Thirty 500 m2 permanent plots were placed
throughout the stand. Within each plot, we collected three soil samples that
were composited and returned to the lab for analysis. Soils were air-dried,
sieved, and assessed for physical and chemical attributes. Sand, silt, clay,
(using hydrometer method) and organic matter (loss on ignition) were all
assessed as a percentage of the total. pH was assessed using a pH probe in a
water:soil slurry and recorded on the standard pH scale of 0-14. Phosphorous,
potassium, magnesium, and calcium were all measured on an atomic absorption
spectrophotometer and recorded as g kg-1. Light was also measured
(at the center of each plot) using hemispherical photographs of the canopy (digital
photographs looking up with a 8mm fisheye lens) and evaluated using a software
application that documents percent open sky, percent direct beam radiation, and
percent diffuse radiation. Do a complete multivariate workup on these data to determine if there are any underlying
environmental gradients that are present in this forest. [40 points]
3. Due to time constraints,
we will be unable to cover one relatively new and useful technique in
multivariate data analysis: Canonical Correspondence Analysis (CCA). This
method is related to CA which we will cover in detail. Basically, CCA allows
for a direct assessment of two matrices simultaneously (usually species x samples
and environment x samples matrices). Using your textbook (McCune & Grace)
first provide a detailed description of what CCA is, how it works, assumptions,
strengths and weaknesses, etc. (i.e., provide a written review of Chpt-21).
There are only three software applications that I am aware of that do CCA:
PC-ORD, CANOCO, and R. Your textbook provides a detailed discussion of the
workings of CCA in PC-ORD. CANOCO is a software application specifically
designed (by ter Braak) to do CCA and is available on some faculty lab
computers. A nice worked example of CCA (by Dave Roberts) using the open source
R code can be found here.
Retrieve your Y data matrix (species x samples) for
the trees of the