Speciation through chromosomal fusion and fission in Lepidoptera

28 Mai 2020
Phylogenetic trees, the chromoSSE script and the input data for the chromoSSE models belonging to the publication "Speciation through chromosomal fusion and fission in Lepidoptera" doi 10.1098/rstb.2019.0539.  For more information, contact jurriaan.devos@unibas.ch or kay.lucek@unibas.ch.

The zipped folder "trees" contains three posterior distributions of chronograms for each of 16 genera, based on a sample of 100 trees each.
Each tree includes the outgroup taxon, and the ingroup-outgroup split was dated based on one of three strategies:
- For the files named GENUS_tmax_pl.tre based on the reported maximum (oldest) age of the reported interval;
- For the files named GENUS_tmed_pl.tre based on the reported median age;
- For the files named GENUS_tmax_pl.tre based on the reported minimum (youngest) age of the reported interval.
Note that the outgroups were pruned prior to diversification rate analysis.
The median age files were used as input for the ChromoSSE analysis; all files were used an input for the analyses based on Brownian Motion.

The file "chromoSSE.Rev" contains a script that runs the cromoSSE models.
Inorder to use this script RevBayes needs to be installed. This can be done by using the link: https://revbayes.github.io/download.
It can be run with the command line:
$> rb chromoSSE.Rev --args 1
As a argument every number between 1 and 16 can be used. And represent a genera:
1 = Colias, 2 = Erebia, 3 = Eunica, 4 = Eurema, 5 = Heliconius, 6 = Ithomia, 7 = Lycaena,
8 = Lysandra, 9 = Memphis, 10 = Morpho, 11 = Oleria, 12 = Papilio, 13 = Pieris,
14 = Polyommatus, 15 = Pteronymia, 16 = Taygetis.
The process runs automatically and generates MCMC outputfiles and stores them in the directory "output".
Each tree that is analyzed returns three files:
-The files named "GENUS.ChromoSSE_anc_statesX.log" logfile of the states;
-The files named "GENUS.ChromoSSE_finalX.tree" tree output of the analysis;
-The files named "GENUS.ChromoSSE_modelX.log" logfile of the model.
The files can be easily accessed by using the software Tracer: https://beast.community/tracer

The zipped folder "data" contains input files needed for the chromoSSE analysis.
To run each analysis a tree "GENUS.pruned.trees" and a tsv-file "GENUS.pruned.states.tsv" with the number of chromosomes per species is needed.
In the trees all species without a chromosom number were excluded.