Data and code for: Host-use Drives Convergent Evolution in Clownfish and Disentangles the Mystery of an Iconic Adaptive Radiation

This folder contains the following files: data/Alignments_WithOutgroups.tar.gz: Contains the alignments of 10,720 genes with the sequences of the outgroup Pomacentrus moluccensis. The gene IDs correspond to the ID of the Amphiprion frenatus reference genome (Marcionetti et al., 2018; https://datadryad.org/stash/dataset/doi:10.5061/dryad.nv1sv). The position of the gene on the Amphiprion percula chromosomes is also reported. For information on the methods and sample names, please refer to the publication. These alignments were used to infer the species tree with ASTRAL-III. Alignments for the genes selected with SortaDate and used for dating with BEAST are also available and are: chr04_g2455.t1.WithOutgroup.phy, chr05_g51486.t1.WithOutgroup.phychr05_g56452.t1.WithOutgroup.phy, chr08_g50086.t1.WithOutgroup.phy, chr09_g35092.t1.WithOutgroup.phy, chr09_g49030.t1.WithOutgroup.phy, chr10_g47484.t1.WithOutgroup.phy, chr11_g5494.t1.WithOutgroup.phy, chr11_g32313.t1.WithOutgroup.phy, chr12_g7961.t1.WithOutgroup.phy, chr12_g27572.t1.WithOutgroup.phy, chr12_g32580.t1.WithOutgroup.phy, chr13_g33152.t1.WithOutgroup.phy, chr15_g60485.t1.WithOutgroup.phy, chr16_g18013.t1.WithOutgroup.phy, chr17_g60288.t1.WithOutgroup.phy, chr22_g6154.t1.WithOutgroup.phy, chr22_g22141.t1.WithOutgroup.phy, chr22_g29206.t1.WithOutgroup.phy, chr23_g36756.t1.WithOutgroup.phy. data/DatedTree.WithOutgroup.tree: BEAST2 output. The clownfish dated phylogenetic tree with the outgroup Pomacentrus moluccensis used for rooting. The tree was obtained with BEAST2, using 20 most informative genes. For each partition, we applied a GTR+ G site model and an uncorrelated relaxed clock with a lognormal distribution. A secondary calibration points was used, setting uniform prior from 10 to 18 MYA for the crown age of clownfishes. For more information on the methods, please refer to the publication. data/Example.DatFile.evolver.tar.gz: Templates of the .dat files (MCcodonNSbranchsites.Shifts_to_Entacmaea.dat, MCcodonNSbranchsites.Shifts_to_Radianthus.dat) containing information to simulate sequences with evolver. The two .dat files were used to simulate sequences under different selection scenarios (no positive selection, convergent positive selection, positive selection on "long" or "clade" branches only) during the shifts to Entacmaeae or Radianthus hosts. The files were used with the scripts Create_DATFile_Evolved.Shift_to_Entacmaea.py and Create_DATFile_Evolved.Shift_to_Radianthus.py to genera