Ladies and gents,
Awesome job powering through the first lab! You will be working with the meristics and morphometrics counts you all collected in Lab 1. For simplicity, I have limited the data to 8 individuals per species. Download the data (“Lab 1 data”) from the class website under “Labs”. With this data, make an ordinationgraph, print it out and paste or staple into your lab notebook.Then, answer the questions below in your notebook (use the two black pages you left between Lab 1 and Lab 2). The data is sorted by the species for you. Graph your data by species, each with a unique color and shape. Please note that the last species is a Rockfish (RCK), not a surfperch! (Optional: you can do the exercise with the full data set (“Lab 1 full data (optional)”) and compare graphs at the end).
Here's how to make the Ordination
1) First, distill all of the data from each individual to just two numbers - one that represents the morphometrics, and one that represents the meristics.
A) For the final morphometrics (lengths) value, first divide each of the morphometrics measurements by the standard length (SL). The number you get will be a ratio (should be between 0 and 1); then, sum those values for a given individual to get your "Morphometrics Composite" variable for each fish.
Morphometric (shape) measurements include:
Standard length (divide other morphometric measurements by this) (*DO NOT divide the standard length by itself).
Eye diameter (ED)
Depth (D)
Snout to dorsal fin (SDF)
Caudal peduncle depth (CPD)
Dorsal fin length (DFL)
Compute your “Morphometrics Composite" in a separate column by adding (sum) these 5measurements.
B) Then, simply sum the meristics counts to get a "Meristics Composite" variable for each fish (no need to divide values here).
Meristic (count) measurements include:
Lateral line scales
Dorsal fin spines
Dorsal fin rays
Anal fin spines
Anal fin rays
Compute your “Morphometrics Composite" in a separate column by adding (sum) these 5measurements (DO NOT divide these by SL).
2) You should now have two values for each of the fishes.From this data, make a scatterplot in Excel (Insert > Chart > XY Scatter).Individualsshould be points, color coded by species, and plotted on a graph where the X AXIS is the MORPHOMETRIC COMPOSITE and THE Y AXIS is the MERISTIC COMPOSITE.
Once you get a blank plot (Insert > Chart > XY Scatter), “select data” by right clicking on the plot or find it on the menu. This may depend on your excel version. Then add one “series” per species (with a plus button). In this case, there will be 7 series to add. Choose a plot style that gives axes labels and a legend for species. Then click on each series and add the species abbreviation (i.e. AAR, HAN) and select the corresponding data in each series/species (again, the morphometric composite should be on the x axisand the meristic composite on the y axis). This should give you a point per individual, colored by species. Now, give a unique shape to each species (square, triangle, circle, etc.). Click in one of the points in the plot, by doing this you are selecting one series, modify the shape (right click on the series, find “Format Data Series”, then find “Marker” and/or “Marker options” and modify the shape). Give every species one unique shape. Axes should be formatted so points fill the graph (right click on the axis, “format axis”, then adjust the max and min).
THE PLOT MUST HAVE A TITLE, LABELED AXES, ONE SERIES PER SPECIES AND THESE SHOULD HAVE A UNIQUE SHAPE. IF YOU DON’T MAKE YOUR OWN GRAPH, YOU WILL NOT GET CREDIT FOR THE QUESTIONS EITHER…
3) This is not a requirement, but I encourage you to try graphs using different "recipes" for the meristic and morphometric composite variables. What happens if you drop the spine counts from meristics? What happens if you drop the eye diameter from morphometrics? Is more data always more informative? If you give this a shot (it is not much extra work), print out your new plot and include in your lab notebook. It may have better resolution of the species than the original!
Questions to be answered in your notebook:
1) Do species overlap in the ordination plot? Can you separate any surfperch from another surfperch? How different is the rockfish in your graph?
—————— Please ignore the rockfish for Questions 2 to 5 —————
2) Are there any outliers? What is the significance of outliers, and how would you interpret them?
3) How much variation is there WITHIN species?
4) What is the major drawback to representing differences in morphology the way we have done (i.e. smashing all of the data together)?
5) Are there any other characters you could have measured or counted that you think would have yielded clearer differences in these species, or others? Would leaving any characters out have yielded a more accurate representation of the differences between species?
DO NOT WAIT TILL LAST MINUTE TO DO THIS. Let us know if you're having trouble with something.