DOI: 10.5061/dryad.d2547d862
title: Geographic isolation alone does not explain divergence of a group of orchid species across Brazil’s campos rupestres sky-islands

description: 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 diversity. When viewed through the lens of
 morphological variability, our study raises intriguing questions about the
 persistence and permeability of species barriers among orchid populations.
 These results, in addition to the recency of the divergence history of B.
 sect. Didactyle, provide insights about hypothesized community level
 versus species-specific paths of diversification across the Neotropical
 sky-islands of the CR.
description: <strong>Bulbophyllum-Didactyle_D40-ind_populations.vcf</strong><br>A VCF file used for calculating population genetics statistics on Stacks. <strong>Bulbophyllum-Didactyle_D25-pop_PCA.structure</strong><br>A structure format file used for reducing the dimensionality and visualizing the dataset including all samples using PCA. <strong>Bulbophyllum-Didactyle_D25-ind_fineRADstructure.radpainter</strong><br>A radpainter format file used for assessing population structure and genetic differentiation on fineRADstructure. <strong>Bulbophyllum-Didactyle_D40U-pop_SVDQ.nex</strong><br>A NEXUS file used for assessing evolutionary relationships using SVDquartets, including all individuals. Individuals were grouped (PAUP’s TaxPartition option) according to geographic/morphologic populations. <strong>Bulbophyllum-Didactyle_D40U-pop-nohyb_SVDQ.nex</strong><br>A 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/morphologic populations. <strong>Bulbophyllum-Didactyle_D40U-ind_SVDQ.nex</strong><br>A NEXUS file used for assessing evolutionary relationships using SVDquartets, including all individuals. <strong>Bulbophyllum-Didactyle_D40U-ind-nohyb_SVDQ.nex</strong><br>A NEXUS file used for assessing evolutionary relationships using SVDquartets. Only individuals without signs of hybridization, based on STRUCTURE analysis, were included. <strong>Bulbophyllum-Didactyle_D40U-ind_RAxML-NG.phylip</strong><br>A PHYLIP file used for assessing evolutionary relationships using RAxML-NG. <strong>Bulbophyllum-Didactyle_D40U-ind-nohyb_RAxML-NG.phylip</strong><br>A PHYLIP file used for assessing evolutionary relationships using RAxML-NG. Only individuals without signs of hybridization, based on STRUCTURE analysis, were included. <strong>Bulbophyllum-Didactyle_D25U-ind-complex_Structure.structure</strong><br>A structure format file used for assessing population structure in the <em>Bulbophyllum exaltatum</em> species complex using the STRUCTURE software. <strong>Bulbophyllum-Didactyle_D25U-pop-complex_IBD.structure</strong><br>A structure format file used for assessing genetic distance among populations from the <em>Bulbophyllum exaltatum</em> species complex on the Isolation by Distance analysis.