Gene flow complicates phylogenetic inference in an archipelago radiation

Allopatric divergence is a fundamental component of most traditional models of biogeography and community assembly. Gene flow between allopatric populations should be influenced by the nature of geographic barriers and can have a profound impact on adaptation, the speciation process, and phylogenetic inference. Superspecies—monophyletic groups of taxa with species-level differences in phenotype or genotype that are found exclusively in allopatry or parapatry—present an opportunity to characterize the effects of gene flow on the divergence process. Here we investigate patterns of gene flow, population structure, and inferred phylogenetic relationships for members of an avian superspecies, the Solomons Monarchs (Aves: Symposiachrus barbatus complex) occupying the Solomon Islands. We found that gene flow among allopatric species matches predictions based on geography, but phylogenetic relationships were not concordant with the most likely colonization history based on a stepping-stone colo..., The dataset is mostly a RAD-seq dataset, generating 1000s of loci across the genome, which were then sequenced on an Illumina sequencer. These were then processed with Stacks, with input generated for downstream analyses using several different scripts outlined in the document. Additionally, we ran two sets of simulations to demonstrate the theorhetical basis of two of our major claims (colonization and the impact of geographically mediated gene flow on phylogenetic inference)., There is a README.txt file included which describes the script and datasets included. Datasets are divided by mode of inference, with scripts associated with given input files (e.g., vcf, phylip, or nexus files) in the same .zip files. I did my best to rename input files in a meaningful way, and change my scripts accordingly, but most scripts aren't designed to run everything with the same directory structure/naming format as the zipped directory (i.e., some alteration needed). Scripts are also uploaded individually to Zenodo. Scripts, accessory files, and trees are also located on my GitHub: https://github.com/ethangyllenhaal/SolomonsSymposRad.
Most figures were edited in Adobe Illustrator to change, e.g., text and line format, but no data were fundamentally altered.
, , README by: Ethan Gyllenhaal
Last updated: 10 Sept 2025

Repository for scripts and input files used in a study investigating gene flow and its impacts on phylogeography in a radiation of Symposiachrus monarch flycatchers in the Solomon islands. Everything is in subfolders within a zipped file. If you use something here, please cite us, or contact EFG on who is best to cite (and remind him if he forgets to update the citation):

This README describes the scripts and data files used for the afforementioned project. The data were collected using Illumina sequencing for RAD-seq libraries, largely following the Stacks reference-based pipeline. Scripts and input data file are in the same folder for a given analysis.

## Useage

The majority of the data included here is output from a Stacks bioinformatics pipeline, which was run as a Torque script on a high performancce computing center. Individual VCFs were then processed with command line tools (e.g., vcftools) or R scripts for preparing fig...