Data from: Phylogenomic analysis of Madagascar’s baobabs reveals admixed populations and supports resurrection of a previously described species
Data files
Jul 16, 2026 version files 14.03 MB
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Dryad_Malagasyplastomes_bombax_mapped.aln
12.12 MB
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Dryad_Malagasyplastomes_bombax_mapped.contree
2.48 KB
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Generate_100reps_forSNaQ.R
9.12 KB
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MalagasyNuclearLociwAlleles.astral
3.40 KB
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NuclearAlignments.zip
1.90 MB
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README.md
2.86 KB
Abstract
Baobab trees are iconic members of Madagascar’s biota that serve as emblems for the island’s unique biodiversity and important targets of conservation efforts. However, despite a long history of research on Malagasy baobabs, more work is needed to evaluate species limits. We use phased allelic sequences derived from custom-designed targeted sequence capture data to clarify the genealogical history of Malagasy baobabs (Adansonia). Using broad geographic sampling, including a few possible hybrid individuals, we reconstructed the population history and used network inference methods to detect reticulation events. We confirmed that one sample from northwestern Madagascar shows admixture between A. rubrostipa and A. madagascariensis. Exclusivity analysis suggests the possibility of elevating subspecific taxa within A. za, and possibly A. rubrostipa, to the species rank, which could result in recognition of seven to eight species in Madagascar rather than the current six. We discuss the implications of gene flow on species delimitation in the context of conservation for these iconic and threatened trees.
https://doi.org/10.5061/dryad.m905qfvbw
Description of the data and file structure
This dataset contains the nuclear and plastid genetic sequences, phylogenetic trees, and scripts required to replicate all analyses in Karimi et al. 2026, accepted in Taxon. We used custom-designed Targeted Sequence Capture baits to generate sequence data for phylogenetic analyses to assess the evolutionary population history of the baobabs, with an emphasis on sampling taxa from Madagascar. We also skimmed the raw reads to assemble complete plastomes. Raw sequence data are available on NCBI SRA, with assembled data for analysis recreation provided here. The nuclear genetic data were used for phylogenetic analyses, exclusivity analysis (per Wright & Baum, 2018), and Phylogenetic Network inference to assess introgression using PhyloNetworks/SNaQ (Solís-Lemus & Ané, 2016).
Below is a summary of the included files:
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Data
File: Dryad_Malagasyplastomes_bombax_mapped.aln; Description: MAFFT Plastome alignments derived from mapping Adansonia skimmed plastome reads to Bombax ceiba MG569974.1.
File: NuclearAlignments.zip; Description: Individual loci which were analysed by maximum likelihood (ML) phylogenetic inference using RAxML v.8.2.10 (Stamatakis, 2014) with the GTR+Γ model and 100 bootstrap (BS) replicates. These alignments were used in downstream analyses.
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Phylogenetic Trees
File: Dryad_Malagasyplastomes_bombax_mapped.contree; Description: Phylogenetic tree inferred using IQ-Tree given the plastome alignment provided above.
File: MalagasyNuclearLociwAlleles.astral; Description: ASTRAL-III tree given the nuclear loci provided above.
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Analysis Scripts
File: Generate_100reps_forSNaQ.R; Description: Custom R script used to generate 100 pseudoreplicate sequence sets given the ML nuclear gene trees for PhyloNetworks.
File: createASTRALmappingFile.Rmd; Description: Read in all gene trees and create an allele mapping file needed as input into ASTRAL
File: CalculatingExclusivityFactors_Karimi2024.Rmd; Description: read in gene trees and calculate exclusivity factors per clade
Access information
Data was derived from the following sources/other publicly accessible locations of the data:
- Additional Dryad repository: http://doi.org/10.5061/dryad.mf1pp3r for Karimi et al. 2019
- Raw reads deposited in the Sequence Read Archive (SRA) of NCBI, BioProject PRJNA579976.
- Transcriptomes available on NCBI Sequence Read Archive under accession PRJNA493960 (Conover et al. 2019).
Bait design, DNA library construction, and captures were performed as previously detailed in Karimi, N., Grover, C.E., Gallagher, J.P., Wendel, J.F., Ané, C. and Baum, D.A., 2020. Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3), pp.462-478.
Read assemblies were performed as previously detailed in Karimi, N., Grover, C.E., Gallagher, J.P., Conover, J.L., Miller, E.R., Wendel, J.F. and Baum, D.A., 2022. Genetic diversity of Malagasy baobabs: implications for conservation. Adansonia, 44(6), pp.37-47.