Evolutionary history of the Mediterranean Pinus halepensis-brutia species complex using gene-resequencing and transcriptomic approaches

172_seqCat_sequences.nex: Concatenated data matrix used for phylogenetic analyses based on 172 resequenced CRIEC loci containing at least five individuals, in which both Pinus brutia and Pinus halepensis are represented together with Pinus taeda as outgroup.

300_seqCat_sequences.nex: Concatenated data matrix used for phylogenetic analyses based on 298 manually verified putative single copy orthologs present in the at least ten samples in the data set containing four Pinus brutia and seven Pinus halepensis individuals as well as the outgroup species Pinus taeda.

PHalBru.cleanSNP.vcf: The final set of filtered 332,915 SNPs, resulting from the joint genotype calling performed simultaneously from the four Pinus brutia and seven Pinus halepensis individuals. 

PHal.cleanSNP.vcf: The final set of filtered 171,932 SNPs, resulting from the joint genotype calling performed simultaneously from the seven Pinus halepensis individuals. 

Brutia.cleanSNP.vcf: The final set of filtered 204,969 SNPs, resulting from the joint genotype calling performed simultaneously from the four Pinus brutia individuals. 

Datasets published in Plant Molecular Biology 2021; https://doi.org/10.1007/s11103-021-01155-7