Multiple bursts of speciation in Madagascar’s endangered lemurs

This dataset contains the following files:
1. Strepsirrhini_AHEsConcatenated_allLoci_allTaxa.nex: This nexus file contains all AHE sequences for all individuals.
2. Strepsirrhini_MitochondrialSequences_cat.nex: This nexus file contains all available mitochondrial sequences from this study.
3. Strepsirrhini_AllIndividuals_AllLoci_RaxmlNG_geneTrees.trees: This file contains gene trees for every AHE locus, as estimated by raxml.
4. GeneTrees_1indvPerGenus_input4Quibl.trees: This file contains the same gene trees as above, but reduced to a single representative per genus (used in Quibl analysis)
5. MCMCTreeFiles_allAnalyses.zip: This zipped file contains a separate folder for each of the 6 MCMCTree analyses performed. Within each folder are all input and output files from these analyses.
6. Strepsirrhini_PhyloNet_InputFiles.zip: This zipped file contains 35 files (7 files for each of the 5 genera analyzed) that were used in PhyloNet analyses. Files are labeled with genus name and with the number of hybrid nodes estimated.
7. 6000TactTrees.trees: This file contains 6000 trees representing 1000 stochastically resolved trees (using the program TACT) for each of the six different fossil calibrated trees.