Data from: Phylogenomic relationships of diploids and the origins of Allotetraploids in Dactylorhiza (Orchidaceae)

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, non-model, polyploid plant complexes.Phylip4DiploidsFigure3.phylip.txtSFiguresSupplementary FiguresSupplementaryTablesSupplementary TablespipelineBioinformatics pipelineBayeasian Factor Delimitation of species for fuchsii-maculataxml filebfd_fuc.xmlBFD for incarnata-euxinaxml file for Bayeasian Factor Delimitation of speciesbfd_inc.xmlPolyRel_2xInput for PolyRelatedness for diploidsPolyRel_4xInput file for PolyRelatedness for allotetraploids.PolyRel_allInput file for PolyRelatedness for all individualsPolyRel_plastidInput for PolyRelatedness for the RADseq locai that localize on the plastid genomesnappSNAPP species treessnapp_MarInput xml file for SNAPPSFigure1.phyPhylip file for RAxML analysi