DOI: 10.5061/dryad.8cz8w9h5p
title: Data from: Geography and admixture shape the genome-scale phylogeny of North American <em>Delphinium</em>

description: The genus Delphinium exemplifies the complexity of plant diversification
 in mountainous regions, where rapid speciation, hybridization, and
 morphological convergence frequently obscure species boundaries. The North
 American lineage Delphinium sect. Diedropetala has rapidly radiated across
 a range of ecological habitats, from alpine tundra to desert grasslands,
 forming an iconic component of western wildflower communities. Despite
 decades of taxonomic study, phylogenetic relationships within this group
 remain poorly resolved. Here, we present a genome-scale phylogeny of 34
 taxa using ddRAD-seq data from 150 individuals sampled across their
 geographic ranges. Our results reveal strong phylogenetic structure
 corresponding to biogeographic regions, including several well-supported
 clades that cut across existing taxonomic subsections, emphasizing the
 need for taxonomic revision. Hybridization and introgression are
 widespread, occurring both within and between these regional clades. Most
 species are connected through a syngameon-like network of introgression,
 with few widespread species acting as central hubs. We describe six
 higher-level clade names and use an agent-based artificial intelligence
 analysis to identify morphological synapomorphies that align with our
 genomic findings. Our study demonstrates that geography and gene flow have
 played a dominant role in shaping the evolutionary history of Delphinium,
 offering a framework for revising its taxonomy and informing future
 conservation efforts.
description: # Data from: Geography and admixture shape the genome-scale phylogeny of
 North American *Delphinium* Dataset DOI:
 [10.5061/dryad.8cz8w9h5p](https://doi.org/10.5061/dryad.8cz8w9h5p) ##
 Description of the data and file structure Phylip formatted sequence
 alignments output by ipyrad: * delphinium-2025.phy * delphinium-2025.snps
 * delphinium-2025-min10.phy * delphinium-2025-min10.snps Raxml-ng
 phylogenetic analysis result files (Newick and log files): *
 {data}.support * {data}.log Caster phylogenetic analysis result files: *
 caster-min4-nomapping-amb1-c500.[nwk,log] *
 caster-min10-nomapping-amb1-c500.[nwk,log] *
 caster-mapping-amb1-c500.[nwk,log] (Note: based on min10 dataset) Fbranch
 results table: * dsuite_caster_min10_fbranch.tsv ### Files and variables
 #### File: delphinium-2025-min10.phy **Description:** "min10"
 sequence alignment from ipyrad requiring data across &gt;= 10 samples per
 site. #### File: delphinium-2025.phy **Description:** "min4"
 sequence alignment from ipyrad requiring data across &gt;= 4 samples per
 site. #### File: caster-min4-nomapping-amb1-c500.log
 **Description:** "min4" caster analysis log file. #### File:
 caster-min10-nomapping-amb1-c500.log **Description:** "min10"
 caster analysis log file. #### File: caster-min4-nomapping-amb1-c500.nwk
 **Description:** "min4" caster analysis newick file. #### File:
 caster-min10-nomapping-amb1-c500.nwk **Description:** "min10"
 caster analysis newick file. #### File: caster-mapping-amb1-c500.nwk
 **Description:** "min10" caster analysis with population mapping
 newick file. #### File: caster-mapping-amb1-c500.log
 **Description:** "min10" caster analysis with population mapping
 log file. #### File: delphinium-2025-min10.phy.raxml.support
 **Description:** "min10" raxml-ng newick file with supports ####
 File: delphinium-2025-min10.phy.raxml.log
 **Description:** "min10" raxml-ng log file #### File:
 delphinium-2025.phy.raxml.support **Description:** "min4"
 raxml-ng newick file with supports #### File:
 delphinium-2025.phy.raxml.log **Description:** "min10" raxml-ng
 log file #### File: delphinium-2025-min10.snps
 **Description:** "min10" phylip file with only snps. #### File:
 delphinium-2025.snps **Description:** "min4" phylip file with
 only snps. #### File: dsuite_caster_min10_fbranch.tsv
 **Description:** dsuite result table using the min10 topology. This table
 is produced by "dsuite" and contains a matrix of f_d scores
 where columns represent introgressive donors and rows are introgressive
 recipients. Taxon combinations that are not possible to test due to the
 phylogenetic tree topology are indicated by "nan" in the matrix.
 For each branch in the "min10" phylogenetic tree, a taxon is
 represented as a row and column by its species-epithet or
 species-epithet+population-ID. Rows contain additional taxa representing
 ancestral branches on the phylogeny that are used to examine the timing of
 introgression, labeled as comma-separated lists of descendant taxon names.
 ## Code/software No software is required to view our data files. * Genomic
 alignments were assembled and written by ipyrad v.0.9.104. * Phylogenetic
 analyses were run in: * raxml-ng v.1.2.1 * caster-site v.1.23.2.6 *
 Introgression analyses were run in Dsuite v.0.5 r58.