One mother for two species: obligate cross-species cloning in ants

This repository contains data for the article "One mother for two species: obligate cross-species cloning in ants".

The content of all folders contained in the ibericusRepository.tar.gz archive is described below.

# Reference genomesThe referenceGenomes folder contains the reference genomes of each species used for fig S7 (time-calibrated phylogeny) with a quast 5.2 report containing various metrics of assembly quality.

# MCMCtree analysesThe mcmctree_dating folder contains the tree with calibrations, and two folders containing the two mcmctree runs with all input and output files.

# Snakemake pipelineThe pipelineSnakemake folder contains a minimal snakefile describing analyses from reads (fastq) to alignments for phylogenetic analyses (including mapping, snp calling, separating maternal/paternal alleles of hybrid individuals, alignments). This folder is not sufficient to re-run all analyses as data are not included in the folder (reads available on GenBank).- the file dag.pdf contains a visual graph of the pipeline connecting the snakemake recipes described in the snakefile. - The file pipelineConda.yaml contains all informations necessary to set up a conda environment with all dependencies and program versions for running analyses (use the command "./mamba_setup.sh pipelineConda.yaml" to setup the corresponding conda environment named pipelineConda).- script folder contains various home-made python script required in the Snakefile.- motherfile.my and runfile.my are config files required by the Snakefile.

# VCF fileThe mainVCF folder contain the vcf file containing all SNPs (before filtering), i.e. the major intermediary file from the snakemake pipeline. Mibericus_genome_ana.busco.fasta contains the BUSCO genes used as reference for mapping all individuals in order to produce the VCF file.

# Phylogenetic analysesThe iqtree_phylogenies folder contains the alignments and resulting phylogenetic tree of figS1, figS2, figS3 and figS7.

# SI4This folder group several sub-folders which are analyses from supplemental information section 4, where we try to better understand the genetic differentiation and gene flow history of the clonal and wild-type lineage of M. structor.