Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single-branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) – a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that proximate chromosomal regions tended to have mor..., , , # Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

[https://doi.org/10.5061/dryad.866t1g1wq](https://doi.org/10.5061/dryad.866t1g1wq)

Give a brief summary of dataset contents, contextualized in experimental procedures and results.

## Description of the data and file structure

This archive contains final data files for every step of the paper \"The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats\". Some intermediate files are not included.
Below is a description of each file in the project directory.
.
├── 01-otomys-typus-asm A directory containing files related to the O. typus assembly
│   ├── abyss\_assembly-contigs.fa The final assembly in FASTA format
│   ├── assembly.conf The configuration file for the assembly containing the local directory with the filtered/trimmed reads (not included in repository; see Methods)
│   ...