REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
HLmyoMyo6	Jebb et al.33	GCA_014108235.1
Myotis myotis Hi-C data	Jebb et al.33	SRR11732436
Myotis myotis ZooFISH map	Volleth et al.34	N/A
Myotis yumanensis reference genome	Curti et al.87	mMyoYum1.0.hap1
Myotis myotis SRA data	Zoonomia Consortium88	SRS3678524
List of differentially expressed genes from a study that treated Myotis daubentonii cell lines with a modified Rift Valley Fever virus or supplemented with IFN to measure response to a viral challenge	Holzer et al.69	Supplementary Material
WGS phylogenomic data generated in this study	This study	PRJNA1035163
WGS data used to generate Myotis myotis recombination map	This study	PRJNA1035163
WGS data used to generate Myotis brandtii recombination map	Laine et al.89	SRR18788643, SRR18788644, SRR18788646, SRR18788647
Myotis myotis recombination map	This study	https://doi.org/10.5281/zenodo.7044479
Myotis brandtii recombination map	This study	https://doi.org/10.5281/zenodo.7044479
Alignments	This study	https://doi.org/10.5281/zenodo.7044479
Newick Tree files	This study	https://doi.org/10.5281/zenodo.7044479
Software and algorithms
Trim Galore! v0.6.5	Krueger et al.90	https://github.com/FelixKrueger/TrimGalore
bwa-mem v0.7.17	Li et al.91; Li92	https://github.com/lh3/bwa
Qualimap	Garcia-Alcalde et al.93	http://qualimap.conesalab.org/
Samtools v1.9	Li et al.94	https://github.com/samtools/samtools
GATK v4.1.2	McKenna et al.95; DePriesto et al.96; Poplin et al.97; Van der Auwera et al.98	https://github.com/broadinstitute/gatk
ANGSD v0.916	Korneliussen et al.56	http://www.popgen.dk/angsd/index.php/Installation
SOAPdenovo2 vr242	Luo et al.98	https://github.com/aquaskyline/SOAPdenovo2
Geneious Prime 2019.04	Dotmatics	https://www.geneious.com/
RYcode	Braun et al.99	https://github.com/ebraun68/RYcode)
IQtree2 v2.2.1	Minh et al.40	https://github.com/iqtree/iqtree2
Quast v5.2.0	Gurevich et al.100	https://github.com/ablab/quast
Bcftools v1.14	Danecek et al.101	https://github.com/samtools/bcftools
VCFtools v1.16	Danecek et al.102	https://vcftools.sourceforge.net/
ReLERNN	Adrion et al.52	https://github.com/kr-colab/ReLERNN
SVDquartets	Chifman and Kubatko39	https://paup.phylosolutions.com/
SNP-sites v2.5.1	Page et al.103	v2.5.1
PAUP∗ v4a168	Posada et al.104	https://paup.phylosolutions.com/
trimAl v1.4.1	Capella-Gutierrez et al.105	https://vicfero.github.io/trimal/
Tree House Explorer (THEx)	Harris et al.61	https://github.com/harris-2374/THEx
R v4.2.2	R Core Team106	https://www.r-project.org/
f(D)	Martin et al.87	https://github.com/simonhmartin/genomics_general
QuIBL	Edelman et al.41	https://github.com/miriammiyagi/QuIBL
STRING v12.0	Szklarczyk et al.87	https://string-db.org/
Dfoil	Pease and Hahn88	https://github.com/jbpease/dfoil
Critical commercial assays
Qiagen Puregene kit	Qiagen	Cat. No./ID: 158063
NEBNext Ultra II DNA Library Prep Kit for Illumina	New England Biolabs	E7805L
NEBNext Multiplex Oligos for Illumina	New England Biolabs	E7600S