Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns

This repository stores data and analyses details of the article entitled : Phylogenomics of Messor harvester ants (Hymenoptera: Formicidae: Stenammini) unravels their biogeographical origin and diversification patterns

#Supermatrix_tree (Fig1)
This folder contains the supermatrix alignment and the iqtree outputs.

#Hybscan (Fig2)
This folder contains the results of specimen heterozygozity scan on UCE's and BUSCO markers, depending on their sequencing type (WGS = BUSCO + UCES; UCE_capture = UCE).

#Mcmctree1 & 2
These folders contain the input and output files for two Markov Chain Monte Carlo, which convergerd and were used for tree datation inference.

#DECx (Fig3)
This folder contains the input and output files for the historical biogeography inference with DECx. 

#Diversification_rates
This folder contains the input and output files for the diversification rates infered with R. 

#Genetrees
This folder contains the file with the iqtree prompts, and all the corresponding gene (UCE) trees.

#Astral (FigS1)
This folder contains the input and output files for generating the gene supertree with weighted ASTRAL-hybrid.

#Concordance_factors
This folder contains the output files of concordance factors computing.