"Evolutionary Paths Underlying Flower Color Variation in Antirrhinum": Difference between revisions

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== Downloading the Project and AAMToolbox ==
=Abstract=
[[Image:HFSP.jpg|thumb||right]]
The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project can be downloaded
[http://www2.cmp.uea.ac.uk/~aih/downloads/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum.zip here]. ''(This contains version 6.5 of the AAMToolbox)''


To create the figures shown in the manuscript “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, ''S. Bensmihen, A. I. Hanna, N. B. Langlade, J. L. Micol, A. Bangham, and E. S. Coen'', HFSP Journal, 2008, please follow the instructions below.
To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.
 
=The Manuscript=
 
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum_Whibley.pdf “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”], ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen''
 
=Downloading the Project and AAMToolbox=
 
 
The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project and the manuscript can be downloaded
[http://cmpdartsvr1.cmp.uea.ac.uk/downloads/papers/EvolutionaryPathsUnderlyingFlowerColorVariationInAntirrhinum.zip here]. ''(This contains version 6.5 of the AAMToolbox)''
 
To create the figures shown in the manuscript “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, ''
A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen'', Science, 313:963-966, 2007, please follow the instructions below.


These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.
These figures were created using ''Matlab 2006b version 7.3.0.267'' running on ''Windows XP''.


==Installing the AAMToolbox==
==Installing the AAMToolbox==
To install the toolbox, simply unzip the zip file you downloaded from the section above. In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Arabid_Antirrh’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
To install the toolbox, unzip the zip file you downloaded from the section above (some unzippers think the file is locked, WinZip and WinRar seem to handle it just fine). In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Science’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
<pre>
<pre>
>>pathtool
>>pathtool
Line 15: Line 26:
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. '''REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL'''.


==Creating Figures==
=Creating Figures=


===Figure 1===
==Figure 4 (f)==
From the Matlab prompt type
<pre>
>>figure_1_points_around_leaf
</pre>


And select ''LE50template_04_05_06.temp_dat'' from the ''Templates'' directory. The colours are your choice.
[[Image:science_wormhole.jpg|300px|thumb|right|An example of the appearance cloud generate for the paper. Figure 4(f)]]
 
Firstly you must make sure that you have correctly installed the Toolshed from [[Computer_programs | here]]. Secondly, you must have downloaded and saved the project '''PRJ_Science''' to your hard disk. If you have done these steps, then start Matlab. In matlab move to project directory '''PRJ_Science''', from the Matlab prompt type
===Figure 2===
From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>
 
* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_18’ for model (Ler only, not scaled).
* Next choose the PCs  you want to display (1 to 5 in our case).
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).
 
===Figure 3===
From the Matlab prompt type
<pre>
<pre>
>>AAMToolbox
>>AAMToolbox
</pre>
</pre>
* Make sure that the current model is “LE50Template_04_05_06\Set_1\ImageList_18” from the drop down list.
This will start the AAMToolbox and if you are in the correct directory you will be presented with the correct details for the project corresponding to this paper.
* Next click the “View Shape Space” button.
* Next click the “Open” button from the Groups panel and select “all_groups_no_tsk”.
* Next click the “Load” button from the Groups panel.
* Next select ‘Tools-Units-Standard Deviations’.
* Next uncheck the “Group Labels” from the plot options panel.
* Next click the “Choose Shape Axes” button and select the PC 1. (To view another PC click the “Choose Shape Axes” button and choose the PC of interest (in our case PC1, PC2, PC3, PC4).)


===Figure 4===
* Click the ''View Shape Space'' button.
'''UNDER CONSTRUCTION'''
* Click the ''Open'' button from the ''Group'' panel.
 
* Select ''SciencePaperGroups.mat'' and click ''Open''.
===Figure 5===
* Click the ''Load'' button from the ''Group'' panel.
From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>
* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_17’ for model (Ler only, scaled).  
* Next choose the PCs you want to display (1 to 4 in our case).  
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).


===Figure 6===
a dialog box with the text ''Loading Group Data, Please Wait..'' will appear, when this dialog box closes you have loaded your groups.
From the Matlab prompt type
<pre>
>>figure_2_pc_effects
</pre>
* Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_21’ for model (_epure= cleaned form double mutant and flower effect mutants).  
* Next choose the PCs you want to display (1 to 4 in our case).  
* Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).


===Figure 7===
* Select ''Tools->Units->Standard Deviations''
'''UNDER CONSTRUCTION'''
* Click the ''Choose App. Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Click the ''Choose Shape Axes'' button from the ''Display Options Panel''
* Select PC's 1, 2 and 3 and click ''Ok''
* Uncheck ''Group Labels'' from the ''Plot Options'' panel


===Figure 8===
* Set dx=30, dy=30 and dz=30 in the ''Surface Quantization'' panel
From the Matlab prompt type
* Click the ''Fit Surface'' button from the ''Display Options Panel''
<pre>
>>AAMToolbox
</pre>
* Make sure that the current model is “LE50Template LE50Template_04_05_06\Set_1\ImageList_21” from the drop down list.
* Next click the “View Shape Space” button.
* Next click the “Open” button from the Groups panel and select “ran_re _double”.
* Next click the “Load” button from the Groups panel.
* Next click the “Choose Shape Axes” button.
* Next select PCs 1 and 2 and hit “Ok”
* Next uncheck “Particles” and “Group Labels” from the “Plot Options” panel.
(The leaf pictures originated from the original pictures (observed). Vectors were added in the Adobe Illustrator CS2 software)


===Figure 9===
a dialog box will appear telling you that the surface has been fitted, close this by clicking ''Ok''.
* Top panel: the outlines of young and mature Arabidopsis and antirrhinum leaves from Yvette’s pictures (for Munderman et al.?) were cut and filled (using the magic stick from Adobe Photoshop). Pictures were copied to Adobe Illustrator CS2 and scaled (selecting your shape, using then from the bar menu: object, transformation, scaling (“mise à l’échelle” in the French version).
* Bottom panel: the outlines of the Arabidopsis and Antirrhinum mean shapes, plus or minus 2SD, were created using the figure_2_pc_effects script as described for Figure 2. The file was saved as .eps and opened in Adobe Illustrator CS2 and the same scaling procedure was used.  


==Creating Tables==
* Check ''Iso-Surface'' box from the ''Plot Options'' panel
* Table 1 originates from the ranked t-test analysis described above performed on all the Arabidopsis Ler groups (on Image List 18 model). Groups were arranged and sorted in XL.
* Slide the ''Isosurface Level'' slider to 3 in the ''Isosurface Pane''
* Table 2 originates  from the ranked t-test analysis (from Image List 21 model) of the antirrhinum groups (E_groups) using as wild type a group of  3 flower mutant groups (“flower_only_formean” group).
* Bring the Appearance window to the front to see the surface.

Latest revision as of 11:51, 24 July 2008

Abstract

To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.

The Manuscript

“Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen

Downloading the Project and AAMToolbox

The project used to create the figures in the manuscript, together with the Matlab toolbox that manages the project and the manuscript can be downloaded here. (This contains version 6.5 of the AAMToolbox)

To create the figures shown in the manuscript “Evolutionary Paths Underlying Flower Color Variation in Antirrhinum”, A. C. Whibley, N. B. Langlade, C. Andalo, A. I. Hanna, J. A. Bangham, and E. S. Coen, Science, 313:963-966, 2007, please follow the instructions below.

These figures were created using Matlab 2006b version 7.3.0.267 running on Windows XP.

Installing the AAMToolbox

To install the toolbox, unzip the zip file you downloaded from the section above (some unzippers think the file is locked, WinZip and WinRar seem to handle it just fine). In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that run the toolbox). The second folder is named ‘PRJ_Science’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type

>>pathtool

Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL.

Creating Figures

Figure 4 (f)

An example of the appearance cloud generate for the paper. Figure 4(f)

Firstly you must make sure that you have correctly installed the Toolshed from here. Secondly, you must have downloaded and saved the project PRJ_Science to your hard disk. If you have done these steps, then start Matlab. In matlab move to project directory PRJ_Science, from the Matlab prompt type

>>AAMToolbox

This will start the AAMToolbox and if you are in the correct directory you will be presented with the correct details for the project corresponding to this paper.

  • Click the View Shape Space button.
  • Click the Open button from the Group panel.
  • Select SciencePaperGroups.mat and click Open.
  • Click the Load button from the Group panel.

a dialog box with the text Loading Group Data, Please Wait.. will appear, when this dialog box closes you have loaded your groups.

  • Select Tools->Units->Standard Deviations
  • Click the Choose App. Axes button from the Display Options Panel
  • Select PC's 1, 2 and 3 and click Ok
  • Click the Choose Shape Axes button from the Display Options Panel
  • Select PC's 1, 2 and 3 and click Ok
  • Uncheck Group Labels from the Plot Options panel
  • Set dx=30, dy=30 and dz=30 in the Surface Quantization panel
  • Click the Fit Surface button from the Display Options Panel

a dialog box will appear telling you that the surface has been fitted, close this by clicking Ok.

  • Check Iso-Surface box from the Plot Options panel
  • Slide the Isosurface Level slider to 3 in the Isosurface Pane
  • Bring the Appearance window to the front to see the surface.