Phase II: Using Our Toolbox

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.title[
# Phase II: Using Our Toolbox
]
.subtitle[
## Module 5: SHARK!
]
.author[
### Dr. Christopher Kenaley
]
.institute[
### Boston College
]
.date[
### 2025/9/29
]

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# In class today

<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.14.0/css/all.min.css">

.pull-left[
Today we'll ....

- Kick off Module 5 (New Phase!!)

- Introduce imageJ/FIJI

- Workflow in Geometric Morphometrics

]

.pull-right[
![](https://upload.wikimedia.org/wikipedia/commons/thumb/3/3c/Full_Shot_of_a_Caribbean_Reef_Shark_at_Tiger_Beach_Bahamas.jpg/1600px-Full_Shot_of_a_Caribbean_Reef_Shark_at_Tiger_Beach_Bahamas.jpg)
]

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## Module 5: First things first

.pull-left[

- Download FIJI
- url: https://imagej.net/software/fiji/downloads

]

.pull-right[

![](https://upload.wikimedia.org/wikipedia/commons/thumb/5/55/FIJI_%28software%29_Logo.svg/1920px-FIJI_%28software%29_Logo.svg.png)
]

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## Module 5: Shark!

.pull-left[

- The Selachii: an ancient radiation
- Body shape: does habitat predict it?

]

.pull-right[
![](https://ars.els-cdn.com/content/image/1-s2.0-S0944200620300581-gr1.jpg)
]

Thomson, Keith Stewart, and Dan E Simanek. 1977. “Body Form and Locomotion in Sharks.” American Zoologist 17 (2): 343–54.

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<center>
<table>
 <tr>
 <td>
 <center>
 <img src="https://earthlife.net/wp-content/uploads/What-Is-A-Elasmobranch-1280x718-1.webp" alt="bull shark" height="150"/> 
 
A white shark, Carcharias carchardon, typical of Group 1.
 
 
</center>
 </td>
 <td>
 <img style="height: 20px; width: 20px"/>
 </td>
 <td>
 <center>
<img src="https://biogeodb.stri.si.edu/sftep/resources/img/images/species/95_8407.jpg" alt="bull shark" height="150"/> 
 
A bull shark, Carcharhinus leucas, typical of Group 2.
 
 
</center>
 </td>
 </tr>
 
 
 
 <tr>
 <td>
 <center>
 <img src="https://upload.wikimedia.org/wikipedia/commons/0/04/Squalus_acanthias_stellwagen.jpg" alt="bull shark" height="150"/> 
 
A dogfish of the genus Squalus typical of Group 3.
 
</center>
 </td>
 <td>
 <img style="height: 20px; width: 20px"/>
 </td>
 <td>
 <center>
<img src="https://biogeodb.stri.si.edu/caribbean/resources/img/images/species/4437_2257.jpg" alt="bull shark" height="150"/> 
 
A kitefin shark, Dalatias licha, typical of Group 4.
 
</center>
 </td>
 </tr>
 
</table>
</center>

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## Module 5: Shark!

.pull-left[

- The Selachii: an ancient radiation
- Body shape: does habitat predict it?
- Sternes & Shimada (2020): only two groups, group B=many pelagic sharks

]

.pull-right[
![](https://ars.els-cdn.com/content/image/1-s2.0-S0944200620300581-ga1_lrg.jpg)
]

Sternes, Phillip C, and Kenshu Shimada. 2020. “Body Forms in Sharks (Chondrichthyes: Elasmobranchii) and Their Functional, Ecological, and Evolutionary Implications.” Zoology 140: 125799.

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## Geometric Morphometrics

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1. Data collection: select landmarks of interest, usually through digitization of specimen images.

2. Data standardization: Make landmarks comparable across all specimens, usually through superimposition.

3. Analysis: choose a statistical approach appropriate to the questions. (Friday)

4. Interpretation: use the outcome of the statistical analysis to assess the original questions. (Friday)

]

.pull-right[
![](https://bcorgbio.github.io/class/shark_points.png)
]

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##  Data collection: FIJI

.pull-left[

- Using multipoint tool, digitize 14 points
- Worflow
- Use macro to save file

![](https://bcorgbio.github.io/class/shark_points.png)

]

.pull-right[
- Open am image.

- Select the multipoint tool.

- Digitize the 14 landmarks you see above.

- Measure the XY positions of these points (cmd/ctrl+m).

- Select the macro tab and run the macro (cmd/ctrl+r).

- Save the results to the appropriate directory.

- Close the results and image tab (don’t save the image).
]

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##  Data collection: FIJI

.pull-left[

- Using multipoint tool, digitize 14 points
- Worflow
- **Use macro to save file**

![](https://bcorgbio.github.io/class/shark_points.png)

]

.pull-right[
### Importance of metadata

```f = getTitle();
dir=getDirectory("Choose where to save data ");
selectWindow("Results");
saveAs("Results", dir+f+"_.csv");
```

Apmel_m0.gif `\(\rightarrow\)` Apmel_m0.gif_.csv

]

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## Data standardization: superimposition

.pull-left[
- generalized Procrustes analaysis (GPA)

![](https://bcorgbio.github.io/class/gpa.png)
]
.pull-right[
![](3140_f25_9-29_files/figure-html/unnamed-chunk-3-1.png)
]