Dive Analysis Lab *If you are using a school computer bring a USB drive to class to save your work and the files for the lab. *If you are using your own computer, make sure to download the data and files before coming to the lab. The purpose of this lab is to introduce you to the tools used to examine the at-sea behavior of marine mammals. You will take data collected from a variety of species and find differences and similarities between species and/or families and draw conclusions based on biology, physiology, and ecology. To look at the at-sea behavior of marine mammals researchers equip animals with time-depth (dive) recorders. These instruments sample many parameters of diving behavior and the environment including: pressure (depth), water temperature, light levels, salinity, and swim velocity. Researchers have the ability to select the variables that are sampled and the rate at which they are sampled. The most recent tags have memory storage of up to 64 Mb. This means that depth, water temperature, and light can be sampled every four seconds for the entire duration of an eight month northern elephant seal foraging migration. Dive recorders are either archival (Wildlife computers, for ex. Mk9) or satellite linked (Sea Mammal Research Unit, SRDL; Figure 1). Archival tags store all of the data collected and need to be recovered (the animal must be recaptured). Satellite linked instruments transmit data through the ARGOS satellite system and animals do not need to be recaptured. Because archival tags have such a large memory they can store precise data points and provide information on a fine scale (seconds). Once archival tags are recovered the instruments are downloaded onto a PC and the analysis begins. Satellite linked tags must summarize data due to the limits of the satellite system so you lose the more detailed information on behavior but data is available in near real time. The type of tag used depends on the study species and the questions the researcher is asking. In this lab you will use data from both types of recorders. Figure 1. Above left is a satellite relay data logger (SRDL). At right is a MK 9 time depth, temperature and light level archival tag (Wildlife Computers, Redmond WA).
LAB PROCEDURES: To Begin: 1) BEFORE YOU OPEN ANY FILES: If you are using a borrowed laptop, make a copy of the Bio129 folder on the desktop and rename it with your last name. All the work you do will be done from this new file and no changes should be made to the original folder! 2) Plot dive profiles. This will give you a qualitative look at the data collected for each species and is what researchers see when they first download data. These are incomplete records since the total size would be too large to plot in excel. Open file Ag raw data.xls in excel. There will be 3 columns labeled Date, Time, and Depth (m). Using the graphing function in excel create a line graph of dive depth vs. time. It should look similar to figure 2. o To make a graph go to Insert on the main menu and select chart. A chart wizard window will open with a selection of chart types. Choose line and for chart subtype select the first graph, click Next. It will ask for a data range. Using your mouse highlight all of the data from the Time and Depth columns. For the next step you can add titles, change axis, move the legend, change background color, etc. This will be valuable for you when you make your final figures for the report. For the last step, decide if you want the chart placed on the page you are working on or in a new worksheet and select Finish. The figure will need some changes made to make it easier to read and more biologically appropriate. o Your graph will need to be modified to look like the figures below. Double click on the y-axis and a Format axis window will open. This window will also be valuable to you when you format your graphs for the report. For now, choose the scale tab. Near the bottom, you will see Values in reverse order and Category (x) crosses at max value. Check both of those boxes and select OK. You can also use this window to change your axis scale. o What patterns do you see in this female s dive behavior? How deep does she dive? Are her dive depths consistent or variable? Does she dive continuously or intermittent? Looking at dive plots we can put together a qualitative description of an animals dive behavior. o Now, make dive plots for the other animals ( Ap raw data.xls, Ma raw data.xls, Nc raw data.xls, Zc raw data.xls, Cu raw data.xls ) to look at the differences in behavior. This is always the first step for researchers. o Qualitatively compare the dive files you have created. How do dive shapes, dive durations, depth, etc. compare between species? Within a dive record how does behavior change with time of day? Use these qualitative comparisons or others to decide what factors you want to examine for your lab report.
Figure 2. Dive plot for an adult female Antarctic fur seal (Arctophoca gazella). 3) Next, all of the files were run through an analysis program (IKNOS, Tremblay unpublished) to measure quantitatively the characteristics of the dive behavior. This provides a list of characteristics for each dive on the record. Below is a description of the how dive characteristics are calculated (Figure 3). Units are provided in parentheses. Maximum dive depth (meters): A Dive duration (sec): B to C (defined by inflection points created by changes in descent and ascent rate) Bottom time (sec): D to E Post dive interval (sec): C to F (end of dive to beginning of next dive) Dive cycle (sec): B to F (one complete dive and the surface interval that follows) Descent rate (m/s): Δ Depth / Δ Time (From B to D) Ascent rate (m/s): Δ Depth / Δ Time (From E to C) Wiggles: 1,2,3,4, etc. Inflection points during bottom time (only useful for mid-water and not benthic feeders) Figure 3. Description of dive characteristic definitions. The solid line profile is a benthic feeder and the dashed dive profile is an epipelagic feeder.
5) For the remaining pinniped excel files ( Ag Female1, Ag Female2, Ag Female3, Ap Female1, Ap Female2, Ap Female3, Ma Female1, Ma Female2, Ma Female3, Nc Female1, Nc Female2, Nc Female3, Zc Female1, Zc Female2, Zc Female3 ) and the cetacean excel files ( Bm 1, Gm 1, Md 1, Oo 1, Pm 1, and Ziphc 1 ) you will have columns set up similar to the following (Table 1): Table 1. Example excel data file for dive data that have been processed using the IKNOS analysis program (Tremblay unpublished). Dive # Date Time (GMT) Max Depth (m) Duration (mm:ss) Post dive interval (hh:mm:ss) Bottom Time (mm:ss) Wiggles Descent Rate (m/s) Ascent Rate (m/s) 1 01/24/05 17:54:42 6 00:32 0:00:00 00:02 0 0.6 0.2 2 01/24/05 18:00:56 3 00:18 0:05:42 00:00 0 0.3 0.2 3 01/24/05 18:01:18 4 00:12 0:00:04 00:04 0 0.6 0.5 4 01/24/05 18:01:50 4 00:06 0:00:20 00:00 0 1.3 0.6 *Note: The files from the crabeater seals (Lc Female1.xls, Lc Female2.xls, Lc Female3.xls) and the leopard seal (Hl 1.xls) do not have a bottom time and wiggles column. 6) The rest is up to you. Develop a hypothesis based on your qualitative assessments and/or material covered in class. Use graphs and basic statistics (mean, maximum, minimum, *your TA will show you how to do this in excel*) to test this hypothesis. Example 1: Based on what you know about diving physiology, dive duration should be related to oxygen stores (and more specifically mass). You can find the average dive depth for each species and compare that to mass. Is there a pattern? What other factors might influence dive depth? These are things you could cover in the discussion. Example 2: Since epipelagic foragers feed on vertically migrating prey you should see a change in dive depth with time of day. Can you determine the foraging pattern of each of the species (epipelagic or benthic)? Your TA will provide other ideas for hypotheses to test. To examine the relationship between dive characteristics it will be useful to make XY scatter plots (dive depth vs. dive duration or dive duration vs. post dive interval). o To make a scatter plot go to Insert on the main menu and select chart. A chart wizard window will open with a selection of chart types. Choose XY (Scatter) and for chart sub-type select the first graph, click Next. It will ask for a data range. Using your mouse highlight all of the data from two columns (dive depth and dive duration, for example). For the next step you can add titles, change axis, move the legend, change background color, etc. This will be valuable for you when you make your final figures for the report. For the last step, decide if you want the chart placed on the page you are working on or in a new worksheet and select Finish (Figure 4).
Figure 4. Relationship between dive depth (m) and duration (min) for an adult female Zalophus californianus. 7) Make sure you save all of your work and any of the files you think you will need for your report onto your disk. You will not have access to these computers after lab section is over. 8) Follow the lab report format (very detailed) to structure your lab report. The lab report format document can be found on the website under the lab portion. Do not hesitate to contact your TA if you have any questions about formatting or what needs to be included in your lab report. A few extra tips: Tables always have the caption at the top (above the table) Figures always have the figure label at the bottom (below the figure) Arial font is a better font to use for figures than times new roman Make sure to make the font of your axis labels large enough to read Exclude any sort of legend unless it is actually necessary for the interpretation of your figure Remove gridlines and background shading from your figures because they are distracting Always italicize species scientific names (i.e. Arctophoca gazella) Label axes clearly with units Make symbols on figures large enough to see but small enough that they do not blur together Use simple colors in figures avoid unnecessary amounts of color and NEVER mix red & green (for those who are colorblind these shades are almost impossible to distinguish) Make sure columns in tables line up nicely and look aesthetically pleasing