Disentangling complex histories of hybridisation: The genomic consequences of ancient and recent introgression in Channel Island monkeyflowers

Hybridization is a common feature of evolutionary radiations, but its genomic consequences vary depending on when it occurs. Since reproductive isolation takes time to accumulate, hybridization can occur at multiple points during divergence. Previous studies suggested that the taxonomic diversity in evolutionary radiations can help infer the timing of past gene flow events. Here, we assess the power of these approaches for revealing when gene flow occurred between two monkeyflower taxa (Mimulus aurantiacus) endemic to the Channel Islands of California. Coalescent simulations reveal that conventional four-taxon tests may not be capable of fully distinguishing between recent and ancient introgression, but genome-wide patterns of phylogenetic discordance vary predictably with different histories of hybridization. Using whole-genome sequencing and phylogenetic tests for introgression across the M. aurantiacus radiation, we identify signals of both ancient and recent hybridization that occur..., Genome sequencing and variant calling 
Leaf tissue from 27 plants was collected across four locations on Santa Cruz Island, California, USA (Table S1), consisting of red-flowered parviflorus, yellow-flowered longiflorus, and their putative hybrids. Tissue was dried in silica in the field, and DNA was isolated using the Zymo Plant and Seed DNA kit following the manufacturer’s instructions. Sequencing libraries were prepared according to Gaio et al (2022), with slight modifications. Bead-linked transposase from the Illumina Nextera XT Kit was used for initial tagmentation, generating insert sizes in the range of 400 – 1200 bp. Multiplexed libraries were sequenced on the Illumina Novaseq 6000 using paired-end 150 bp reads at the University of Oregon’s Genomics Core Facility.
New sequences from Santa Cruz Island were combined with previously generated whole genome sequences from various M. aurantiacus subspecies from Stankowski et al. (2019) and Short & Streisfeld (2023), resulting..., # Disentangling complex histories of hybridisation: The genomic consequences of ancient and recent introgression in Channel Island monkeyflowers

Dataset DOI: [10.5061/dryad.cfxpnvxjw](10.5061/dryad.cfxpnvxjw)

## Description of the data and file structure

In this study we set out to examine the history and outcomes of introgression between a pair of parapatric, monkeyflower subspecies that are endemic to the Channel Islands of California. To do this we generated sequence data from leaf tissue collected from 27 plants across four locations on Santa Cruz Island, California, USA. These sequenced plants included red-flowered *parviflorus*, yellow-flowered *longiflorus*, and their putative hybrids. DNA was extracted from these leaves and sequenced using an Illumina Novaseq 6000. These 27 whole genome sequences were then combined with previous whole genome sequences generated from various members of the *Mimulus aurantaicus* species complex (Stankowski et al. 2019). To identify hybrid indiv...,