1. Questions
Do fish species differ in relative abundance as a function of zone (shallow, deep)
This should be in the context of a specific set of predictions based on difference in depth, physical and biological attributes associated with depth, ecological understanding (e.g. gopher vs black and yellow rockfish) and theory that links these to relative abundance of these species. Predictions should have been motivated in Introduction
Does species accumulation differ as a function of zone
Again, this should be in the context of a specific prediction and theory (i.e. concerning species richness and evenness) Predictions should have been motivated in Introduction.

2. Data Collection
Fish data were collected along 30 meter transects in the deep and shallow zones at Hopkins. Data were collected in 5 meter segments.

3. Physical Attributes
Substrate: These data were collected in the UPC surveys. There are 4 categories: SA=sand, CO-cobble, BO=boulder, BR=bedrock. Shown is the relative abundance of each as a function of zone.
Relief: These data were also collected in the UPC surveys. There are 4 categories: There are 4 categories: F=flat, S=slight or shallow, M-moderate, H=high. Shown is the relative abundance of each as a function of zone.

4. Substrate as a function of Zone

5. Relief as a function zone

6. Biological Attributes
Macrocystis and Cystoseira abundance: These data were collected in the swath surveys. Shown is the relative abundance of each species as a function of zone.

7. Macrocystis and Cystoseira as a function of depth

8. Relative abundance of Species
Two graphs are shown.
First the density of fish per transect by species and by zone.
Second the same data were used to graph the relative abundance of fish by species and by zone (the percentages in a zone add to 100).
The analysis done was a chi square analysis. This is done on the raw number of observation. It is a test of independence of the predictor variables, here these are species and zone. The null hypothesis is that species abundance and zone are independent. This means that there should be no difference in the relative abundance of the species as a function of zone. If the p-value is significant it is an indication that species and zones are not independent, that is, that the relative abundance of the species varies by zone

9. Fish density as a function of Zone
Test Statistic
Value df
p-Value
Pearson Chi-Square
<

10. Fish composition as a function of Zone

11. Species accumulation graphs
These are based on re-sampling theory.
The lines indicate the expected number of species that would be found as a function of number of segments sampled. Each value (Number of species) represents the best estimate for the defined number of segments. This value is obtained by resampling the data.
For example for number of points=5, groups of 5 segments are randomly selected and the number of species found in those 5 segment points is determined. This is done over and over (typically 100 times per defined number of segments) in order to produce a robust estimate of likely number of species for any give set of segments. This method produces a very smooth relationship.
You should think about the lines in terms of the asymptote, which is essentially the maximum number of species found and the initial slope, which is an indication of the how common certain species are.
A location with a few common species and many rare ones will have a lower initial slope than another location with the same number of species but all about the same abundance. Hence, the greater the initial slope the more even the species abundances are.
Recall that diversity is a measure of species richness and evenness. Given this, a zone is more diverse than another if its initial slope and asymptotic values is greater than another zone.

12. Number of species as a function of number of segments sampled