Data and code from: A multifaceted approach reveals complex genomic mediation of white-nose syndrome resistance in the little brown bat (<em>Myotis lucifugus</em>)

Novel pathogens have become a major challenge faced by wildlife in the Anthropocene. White-nose syndrome (WNS), a fungal pathogen, has decimated bat populations across North America over the last two decades. Demographic and physiological evidence of resistance in one heavily affected species, Myotis lucifugus, has prompted multiple attempts to delineate the genomic underpinnings, but they show little congruence in their findings. This may be due, in part, to the limitations of the genomic resources utilized and/or analytical approaches employed. Here, we performed high-coverage whole-genome resequencing of M. lucifugus sampled prior to (n = 29) and 10 years after the arrival of WNS (n = 30), aligned to a new reference genome to identify signatures of selection associated with pathogen resistance. Using 41.9 million SNPs, we implemented a combination of hard and soft sweep detection analyses, leading to discovery of 405 genes with robust evidence of selection. Of these, 241 (59.5 %) wer..., , , # README: A multifaceted approach reveals complex genomic mediation of white-nose syndrome resistance in the little brown bat (*Myotis lucifugus*) Dataset DOI: [10.5061/dryad.ncjsxkt66](https://doi.org/10.5061/dryad.ncjsxkt66) ## Description of the data and file structure This dataset contains all analytical code for this manuscript, along with associated data files, two versions of the final VCF, and selection statistic output files. The genome annotation used with this data is available through [https://github.com/docmanny/myotis-gene-annotations](https://github.com/docmanny/myotis-gene-annotations). ## Data Files #### VCFs: * **gatk.snp.qual_hard_filtered_autosomes.vcf.gz** -- full set of filtered SNPs * **gatk.snp.qual_hard_filtered_autosomes_thin.vcf.gz** -- filtered SNPs thinned by 10 Kbp distance #### SNP Calling Pipeline Input Files: * **RG_info.tsv** -- read group information for variant calling * **all_samples.txt** -- sample IDs for all individual FASTQ files * **all_...,