Speciation through chromosomal fusion and fission in Lepidoptera

<p>28 Mai 2020<br> Phylogenetic trees, the chromoSSE script and the input data for the chromoSSE models belonging to the publication &quot;<strong>Speciation through chromosomal fusion and fission in <em>Lepidoptera&quot; </em></strong>doi 10.1098/rstb.2019.0539.&nbsp; For more information, contact jurriaan.devos@unibas.ch or kay.lucek@unibas.ch.</p> <p>The zipped folder &quot;trees&quot; 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.</p> <p>The file &quot;chromoSSE.Rev&quot; 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 &quot;output&quot;.<br> Each tree that is analyzed returns three files:<br> -The files named &quot;GENUS.ChromoSSE_anc_statesX.log&quot; logfile of the states;<br> -The files named &quot;GENUS.ChromoSSE_finalX.tree&quot; tree output of the analysis;<br> -The files named &quot;GENUS.ChromoSSE_modelX.log&quot; logfile of the model.<br> The files can be easily accessed by using the software Tracer: https://beast.community/tracer</p> <p>The zipped folder &quot;data&quot; contains input files needed for the chromoSSE analysis.<br> To run each analysis a tree &quot;GENUS.pruned.trees&quot; and a tsv-file &quot;GENUS.pruned.states.tsv&quot; with the number of chromosomes per species is needed.<br> In the trees all species without a chromosom number were excluded.</p>