Geographic isolation alone does not explain divergence of a group of orchid species across Brazil’s campos rupestres sky-islands
Data files
Jan 19, 2023 version files 403.56 MB
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Bulbophyllum-Didactyle_D25-ind_fineRADstructure.radpainter
4.72 MB
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Bulbophyllum-Didactyle_D25-pop_PCA.structure
16.37 MB
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Bulbophyllum-Didactyle_D25U-ind-complex_Structure.structure
2.08 MB
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Bulbophyllum-Didactyle_D25U-pop-complex_IBD.structure
2.27 MB
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Bulbophyllum-Didactyle_D40-ind_populations.vcf
368.04 MB
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Bulbophyllum-Didactyle_D40U-ind_RAxML-NG.phylip
1.83 MB
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Bulbophyllum-Didactyle_D40U-ind_SVDQ.nex
1.84 MB
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Bulbophyllum-Didactyle_D40U-ind-nohyb_RAxML-NG.phylip
1.52 MB
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Bulbophyllum-Didactyle_D40U-ind-nohyb_SVDQ.nex
1.52 MB
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Bulbophyllum-Didactyle_D40U-pop_SVDQ.nex
1.84 MB
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Bulbophyllum-Didactyle_D40U-pop-nohyb_SVDQ.nex
1.52 MB
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README.md
2.76 KB
Abstract
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.
Bulbophyllum-Didactyle_D40-ind_populations.vcf
A VCF file used for calculating population genetics statistics on Stacks.
Bulbophyllum-Didactyle_D25-pop_PCA.structure
A structure format file used for reducing the dimensionality and visualizing the dataset including all samples using PCA.
Bulbophyllum-Didactyle_D25-ind_fineRADstructure.radpainter
A radpainter format file used for assessing population structure and genetic differentiation on fineRADstructure.
Bulbophyllum-Didactyle_D40U-pop_SVDQ.nex
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.
Bulbophyllum-Didactyle_D40U-pop-nohyb_SVDQ.nex
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.
Bulbophyllum-Didactyle_D40U-ind_SVDQ.nex
A NEXUS file used for assessing evolutionary relationships using SVDquartets, including all individuals.
Bulbophyllum-Didactyle_D40U-ind-nohyb_SVDQ.nex
A NEXUS file used for assessing evolutionary relationships using SVDquartets. Only individuals without signs of hybridization, based on STRUCTURE analysis, were included.
Bulbophyllum-Didactyle_D40U-ind_RAxML-NG.phylip
A PHYLIP file used for assessing evolutionary relationships using RAxML-NG.
Bulbophyllum-Didactyle_D40U-ind-nohyb_RAxML-NG.phylip
A PHYLIP file used for assessing evolutionary relationships using RAxML-NG. Only individuals without signs of hybridization, based on STRUCTURE analysis, were included.
Bulbophyllum-Didactyle_D25U-ind-complex_Structure.structure
A structure format file used for assessing population structure in the Bulbophyllum exaltatum species complex using the STRUCTURE software.
Bulbophyllum-Didactyle_D25U-pop-complex_IBD.structure
A structure format file used for assessing genetic distance among populations from the Bulbophyllum exaltatum species complex on the Isolation by Distance analysis.
- Fiorini, Cecilia F; Borba, Eduardo Leite; Resende-Moreira, Luciana C et al. (2023). Geographic isolation alone does not explain divergence of a group of orchid species across Brazil’scampos rupestressky-islandsIsolamento geográfico por si só não explica a divergência de um grupo de espécies de orquídeas nos campos rupestres do Brasil. Evolution. https://doi.org/10.1093/evolut/qpad010
