Speciation through chromosomal fusion and fission in Lepidoptera

28 Mai 2020<br> Phylogenetic trees, the chromoSSE script and the input data for the chromoSSE models belonging to the publication "<strong>Speciation through chromosomal fusion and fission in <em>Lepidoptera" </em></strong>doi 10.1098/rstb.2019.0539. For more information, contact [e-mail] or [e-mail]. The zipped folder "trees" contains three posterior distributions of chronograms for each of 16 genera, based on a sample of 100 trees each.<br> Each tree includes the outgroup taxon, and the ingroup-outgroup split was dated based on one of three strategies:<br> - For the files named GENUS_tmax_pl.tre based on the reported maximum (oldest) age of the reported interval;<br> - For the files named GENUS_tmed_pl.tre based on the reported median age;<br> - For the files named GENUS_tmax_pl.tre based on the reported minimum (youngest) age of the reported interval.<br> Note that the outgroups were pruned prior to diversification rate analysis.<br> 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.<br> Inorder to use this script RevBayes needs to be installed. This can be done by using the link: https://revbayes.github.io/download.<br> It can be run with the command line:<br> $&gt; rb chromoSSE.Rev --args 1<br> As a argument every number between 1 and 16 can be used. And represent a genera:<br> 1 = Colias, 2 = Erebia, 3 = Eunica, 4 = Eurema, 5 = Heliconius, 6 = Ithomia, 7 = Lycaena,<br> 8 = Lysandra, 9 = Memphis, 10 = Morpho, 11 = Oleria, 12 = Papilio, 13 = Pieris,<br> 14 = Polyommatus, 15 = Pteronymia, 16 = Taygetis.<br> The process runs automatically and generates MCMC outputfiles and stores them in the directory "output".<br> Each tree that is analyzed returns three files:<br> -The files named "GENUS.ChromoSSE_anc_statesX.log" logfile of the states;<br> -The files named "GENUS.ChromoSSE_finalX.tree" tree output of the analysis;<br> -The files named "GENUS.ChromoSSE_modelX.log" logfile of the model.<br> 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.<br> 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.<br> In the trees all species without a chromosom number were excluded.