monophyly_permutation

Geographical component of the panel structure (Figure 2A)

Author: Wandrille Duchemin

Code and data for the permutation tests to test the grouping of three character : continent of origin, growth habit, and historical group.

Basis for Figures and Tables

• Figure 2A

Workflow

1. Extract clades

script to list all clades in a tree Code:

• extract_all_clades.py

Input

• hexaploid wheat phylogenetic tree ( eg. this tree )

Output

prints to screen the list of clades in the unrooted tree. One line per clade, leaf names separated by ";".

See allHexaClades.txt.

2. Determining the most structuring character, using proportion of monophyletic clades and permutation tests

Input:

1. Phylogenetic clades to test allHexaClades.txt
2. Genotype metadata Sup_487samples.csv
3. Character trait i.e. name of the column to use as a trait from the second file:
   • "Growth habit"
   • Group
   • Continent
4. Number of permutations
5. Filename to direct output to e.g. allHexaClades.txt.Growth_habit.PermutsPmonophyletic.100

Output:

Prints to screen the proportion of clades which are monophyletic for the given character in the original data, as well as the number (and proportion) of sampled permutations which show a higher proportion of monophyletic clades. Also writes a file (e.g. allHexaClades.txt.Growth_habit.PermutsPmonophyletic.100) containing the proportions of monophyletic clades of the sampled permutations (1 floating number per line).

Code:

• computeMonophyly.py

Command example, 100 permutations for the Growth Habit character trait :

python computeMonophyly.py allHexaClades.txt Sup_487samples.csv "Growth habit" 100 allHexaClades.txt.Growth_habit.PermutsPmonophyletic.100

prints to screen:

proportion of monophyletic :  0.31870669746
original data shows more monophyletic clades than 100.0 ( 1.0 ) permutations.

and creates a file named allHexaClades.txt.Growth_habit.PermutsPmonophyletic.100 which contains 100 floating numbers.

Results

• Growth habit : proportion of monophyletic : 0.31870669746
• Group : proportion of monophyletic : 0.322748267898
• Continent : proportion of monophyletic : 0.384526558891

We performed 10 000 000 permutations each for each character.

• allHexaClades.txt.Growth_habit.PermutsPmonophyletic.txt.10M no permutation with a proportion > 0.31870669746 -> p-value < 10-7
• allHexaClades.txt.Group.PermutsPmonophyletic.txt.10M no permutation with a proportion > 0.322748267898 -> p-value < 10-7
• allHexaClades.txt.Continent.PermutsPmonophyletic.txt.10M no permutation with a proportion > 0.384526558891 -> p-value < 10-7