Geographic isolation alone does not explain divergence of a group of orchid species across Brazil’s campos rupestres sky-islands

Mountains play a crucial role in the origin and maintenance of Neotropical biodiversity, but there are still unanswered questions about the diversification of the campos rupestres (CR), an herbaceous-shrubby sky-island vegetation in Eastern South America. For orchids distributed across this disjunct rock habitat, difficulties with distinguishing morphological taxa add an additional challenge to disentangling the history of divergence. Here, we combined the power of ddRAD genomic data with broad sampling of Bulbophyllum sect. Didactyle (Orchidaceae), across the CR and other Neotropical outcrops, to estimate evolutionary relationships and reconstruct the biogeography of the group’s diversification. Although genetic lineages generally align with geographic disjunctions, we also observe distantly related lineages within some previously recognized species. For such taxa, their lack of monophyly and a shared regional divergence pattern suggests a complex history that may include unrecognized ..., , Bulbophyllum-Didactyle_D40-ind_populations.vcfA VCF file used for calculating population genetics statistics on Stacks.
Bulbophyllum-Didactyle_D25-pop_PCA.structureA structure format file used for reducing the dimensionality and visualizing the dataset including all samples using PCA.
Bulbophyllum-Didactyle_D25-ind_fineRADstructure.radpainterA radpainter format file used for assessing population structure and genetic differentiation on fineRADstructure.
Bulbophyllum-Didactyle_D40U-pop_SVDQ.nexA NEXUS file used for assessing evolutionary relationships using SVDquartets, including all individuals. Individuals were grouped (PAUP’s TaxPartition option) according to geographic/morphologic populations.
Bulbophyllum-Didactyle_D40U-pop-nohyb_SVDQ.nexA NEXUS file used for assessing evolutionary relationships using SVDquartets. Only individuals without signs of hybridization, based on STRUCTURE analysis, were included. Individuals were grouped (PAUP’s TaxPartition option) according to geographic/...