The role of breakpoint mutations, supergene effects, and ancient nested rearrangements in the evolution of adaptive chromosome inversions in the yellow monkey flower, Mimulus guttatus

Large chromosomal inversion polymorphisms are ubiquitous across the diversity of diploid organisms and play a large role in the evolution of adaptations in those species. Despite their importance, the underlying mechanisms by which inversions produce their adaptive phenotypic effects and become geographically widespread are still poorly understood. One way inversions could cause phenotypic effects is through meiotic recombination suppression, which can result in the formation of a supergene containing linked adaptive alleles. This supergene hypothesis has been promoted by theoreticians, but thus far, no studies have definitively identified multiple linked adaptive genes within an inversion. Alternatively, according to the breakpoint mutation hypothesis, the inversion mutation itself could result in adaptive phenotypic effects if it disrupts genes or alters the regulation of nearby genes. Here, we evaluate both of these hypotheses using new long-read sequencing-based genomes of the yello..., , , # **Mimulus guttatus inland annual and coastal perennial genome assembly and associated files**

**[https://doi.org/10.5061/dryad.2ngf1vhwj](https://doi.org/10.5061/dryad.2ngf1vhwj)**

These datasets are the result of long read Oxford Nanopore Technologies (ONT) genome assemblies. We assembled genomes for an individual from the inland annual (LMC) and an individual from the coastal perennial ecotype (SWB). We used these genomes to identify chromosomal inversion breakpoint regions, call single nucleotide polymorphisms (SNPs), identify structural variants (SVs), and run differential expression and population genetic analyses on previously published datasets.

## **Description of the data and file structure**

### **Genome assemblies and annotations**

1. Mimulus_guttatus.SWB-S1-2.v1.fa- SWB-S1 genome assembly (pseudochromosomes)
2. Mimulus_guttatus.LMC-L1-2.v1.fa- LMC-L1 genome assembly (pseudochromosomes)
3. Mimulus_guttatus.LMC-L1-2.v1.2.gff - LMC-L1 genome annotation file
4. Mimulus_gu...