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NZ_Rotifera

Aim

All data files and scripts to recreate figures from the paper

1. Create the map of NZ with collection locations

Script: 01_collection_sites.R

Input: 01_NZ_Rotifer_sites.csv

Output: (ggsave) --> inkscape --> 01_collection_sites.png

2. Create the tree using IQ-TREE v2.2.0

IQ-TREE command: bin\iqtree2 -s 02_alignment.phy -B 1000 -nm 3000 -bnni -T AUTO -m MFP

Input: 02_alignment.phy

Outputs: 02_tree.treefile, 02_IQ-tree.log

3. Create the overall phylogenetic tree, and a set of trees for each genus

Script: 03_tree_vis.R

Inputs: 02_tree.treefile, 03_metadata.csv, 03_genus_list.csv

Outputs: supplementary_full_tree.pdf, subtree_{genus}.pdf

4. Perform the barcode gap analysis

Script: 04_barcode_gap_analysis.R

Inputs: 04_metadata_for_barcode_gap.csv, 04_alignment_for_barcode_gap.fasta

Outputs: 04_distmatrix.csv, 04_barcode_gap_results.csv, 04_barcodegap.png

5. Perform the GMYC analysis

5a create ultrametric bifurcating tree in BEAST

BEAUti priors: 05a_priors.xml

Run this twice in BEAST

Combined the two outputs into one new tree: 05a_ultrametric.tree

5b GMYC analysis in R

Script: 05b_GMYC.R

Input: 05a_ultrametric.tree

Outputs: 05b_species_list.csv, 05b_yulesupport.csv

Note: added the species list column back to the original 03_metadata.csv file and replotted the tree with this information in tip labels

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