Budding speciation involves isolation of marginal populations at the periphery of a species range and is thought to be a prominent mode of speciation in organisms with low dispersal and/or strong local adaptation among populations. Budding speciation is typically evidenced by abutting, asymmetric ranges of ecologically-divergent sister species and low genetic diversity in putative budded species. Yet these indirect patterns may be unreliable, instead caused by post-speciation processes such as range or demographic shifts. Nested phylogenetic relationships provide the most conclusive evidence of budding speciation. A putative case of budding speciation in the serpentine endemic Clarkia franciscana and two closely related widespread congeners was studied by Harlan Lewis, Peter Raven, Leslie Gottlieb and others over a 20-year period, yet the origin of C. franciscana remains controversial. Here, we reinvestigate this system with phylogenomic analyses to determine whether C. franciscana is a recently derived budded species, phylogenetically nested within one of the other two putative progenitor species. In contrast to the hypothesized pattern of relatedness among the three Clarkia species, we find no evidence for recent budding speciation. Instead, the data suggest the three species diverged simultaneously. We urge caution in using contemporary range patterns to infer geographic modes of speciation.

This is a phylogenomic dataset, composed of 24 taxa and ultimately 233 loci. An enriched genomic sequencing approach was used; a bait set was designed from single-copy genes in a related species. 

In this paper, we processed raw reads (sorting reads into gene directories and aligning within directories), aligned and trimmed gene sequences, built a variety of gene trees and species trees, and analyzed discordance among methods of species trees interest, and among gene trees and species trees. 

All .R and .Rmd files are to be opened in R (https://www.r-project.org) or Rstudio (https://posit.co/downloads/). 

To view phylogenetic tree files (.tree), I use the free program FigTree (v1.4.4) (http://tree.bio.ed.ac.uk/software/figtree/)

The .svg output files from the PhyParts analysis can be viewed in any major browser (Chrome, Safari, Firefox, etc.).

All other files (e.g., .txt, .fa, .fasta, .py, .sh, .pl, .raxml, .err, .out, .SSLL, .no_outliers, .concord.node*, .conflict.node*, .hist, .hist.alts, .node.key) can be viewed in your favorite text editor. I use BBedit (https://www.barebones.com/products/bbedit/). Please refer to the detailed "Code_workflow.txt", and "Code_by_steps" and "Data_Outputs" directories to see how these files are used in analyses.