data sets and trees for the Rasplus et al paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020)

Data sets and trees for the Rasplus et al. paper "Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)" Cladistics (2020). Preprint = https://www.biorxiv.org/content/10.1101/2020.04.15.042259v1

*.phy = Data sets (phylip format) [see Table 2 of the paper for more details].

- mergeR1R2.phy : complete data set (530 RAD loci shared by 75% of the samples + assembly of forward & reverse reads)
- mergeR1R2_GCinfmean.phy : loci with GC content inferior or equal to mean GC content
- mergeR1R2_GCsupmean.phy : loci with GC content strictly superior to mean GC content
- mergeR1R2_LS3.phy : loci that evolve at a homogeneous rate across clades of interest (Clade1= sect. Pharmacosycea; Clade2=subg. Urostigma, Clade3=sect. Oreosycea, Clade4= "gynodioecious clade")
- mergeR1R2_PCA.phy : loci for which difference between Long Branch (LB) scores for sect. Pharmacosycea and other ingroups was not significant according to our custom iterative PCA approach

 
Fig*.nwk : Trees (newick format) that were obtained for the different data sets.

Trees are also included as Figures or Supplementary Figures of the paper. Note that you may visualize these nwk trees in FigTree (open FigTree. Upload the FigS1A_RAxML_mergeR1R2_inclfigtreeannot.nex first and then open the other trees - do not close FigTree in between !- Annotations included in the first file will be automatically used to annotate other trees).   

Appendix S2 : Morphological matrix + morphological tree + 4 competing molecular trees.

This file can be opened in Mesquite to get reconstruction of ancestral character states