Related paper: Conservation genomics insights into the spontaneous integration of multiple reproductive strategies in an endangered citrus relative
Using citrus (wild kumquat and cultivate kumquat populations) to study conservation genomics, especially the geogracial location, introgression and the mating systems.
A R script for ecological prediction of kumquats using BIOMOD2
A R script for ecological prediction of kumquats using MAXENT
A R script for ecological niche overlap of kumquat populations using nicheROVER
The values (bio1-19) in cultivated population
The values (bio1-19) in wild population
A R script for tranform tif to csv
A python script for estimate phylogenetic trees
A python controled script for smc pipeline (need docker env)
rho dataset in chr1 of wild kumquat population
performed biaplot in R
The apomictic individual ‘DB’ heterozygous peaks in chr1
The sexual reproducing individual ‘DR01’ heterozygous peaks in chr1
The python script for genome-wide heterozygous peaks.
The scripts, for instance, SSMs could find in https://github.com/wangnan9394/apomixis_parallel_evolution
The docker ENV (version) were listed in used_docker.list