Data from: Reconstructing historical processes that underlay the diversification of Amsonia (Apocynaceae)
Data files
May 08, 2026 version files 81.84 MB
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Amsonia_Astral_input.tre
1.53 MB
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Amsonia_Beast_input.nex
2.27 MB
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Amsonia_Concatenated_input.phy
78.04 MB
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README.md
1.01 KB
Abstract
Here we are submitting the processed alignment files that were used to create 1) the Astral method phylogeny, 2) the concatenated method phylogeny, and 3) the input for BEAST. We note that the output of BEAST was then used to estimate ancestral areas and also habitat reconstruction.
Dataset DOI: 10.5061/dryad.n02v6wxck
Description of the data and file structure
Files and variables
File: Amsonia_Beast_input.nex
Description: This input was used to estimate divergence times.
File: Amsonia_Astral_input.tre
Description: This input was used to estimate a coalescent species tree.
File: Amsonia_Concatenated_input.phy
Description: This input was used to estimate a concatenated phylogeny.
Code/software
Any of these files can be viewed using a simple text editor like bbedit or others. The concatenated dataset (.phy) is formatted and ready to be run with IQ-TREE for Maximum likelihood analysis. The Astral dataset is formatted (.tre) for input into Astral and the b tree is formatted for use with any version of beast. All of these programs are freely available online for download.
This data was collected by extracting DNA from silica dried leaf material collected from the wild and also from sampling herbarium voucher specimens. A target capture approach was used along with the Angiosperm 353 Bait set. Libraries were created in house and sequenced on a NovaSeq machine at Northwesterns Medical campus in Chicago. Upon receiving the raw data we cleaned it used Trimmomatic and Cutadapt and then processed using HybPiper. Raw sequences were further processed using HybPhaser and then aligned using mafft. The concatenated dataset represents all genes that have been combined into a single file and aligned. The Astral data set represents the phylogenetic trees produced for each gene individually after running iqtree. This formated to run with Astral. Lastly we have are one tip species tree with outgroups, formatted for Beast Analysis. Please see our paper for more detailed methods or email the first author.