Repeated waves of colonization of a great speciator

Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones—where reproductive isolation can further develop via reinforcement or phenotypic displacement—or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr’s foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resultin..., This manuscript is primarily based on a RAD-seq dataset, with supplementary ultraconserved element target capture data. The RAD-seq data was processed with Stacks, and UCE data with phyluce. The RAD data was used for a variety of phylogeographic analysis, including ones investigating population structure, phylogeny, divergence landscape, and gene flow. This upload includes a README that details scripts used to produce data, some intermediate files, and final outputs., , README by: Ethan Gyllenhaal
Last updated: 14 April 2025

Repository for scripts and input files used in a study investigating the phylogeographic history of Pachycephala whistlers in Fiji. Everything is in subfolders within a zipped file. If you use something here, please cite us.

This README describes the scripts and data files used for the aforementioned project. The data were collected using Illumina sequencing for RAD-seq libraries, largely following the Stacks reference-based pipeline. Data uploaded to Dryad is in zipped directories outlined below, code relevant to analyses is under the relevant section but stored on Zenodo ([https://doi.org/10.5281/zenodo.12774334](https://doi.org/10.5281/zenodo.12774334)) and github ([https://github.com/ethangyllenhaal/FijiPachyRad)](https://github.com/ethangyllenhaal/FijiPachyRad\)). Code stored on Github and Zenodo is denoted by ***.

## Usage

The majority of the data included here is output from a Stacks bioinformatics pipeline, which was ru...,