Genotyping-by-sequencing Single-nucleotide Polymorphism Dataset for Corynorhinus rafinesquii (CORA) and Myotis austroriparius (MYAU)

Understanding underlying genetic structure is essential for the conservation and management of rare or uncommon species because it is important to protect their evolutionary potential and adaptability by preserving genetic diversity. Southeastern Myotis (Myotis austroriparius or MYAU) is an uncommon bat species that ranges across much of the southeastern United States. At the state level, MYAU is regarded as endangered or a Species of Greatest Conservation Need across nearly all its distribution. The overall objective of this study was to examine the genetic structure and genetic diversity of MYAU by determining levels of subpopulation connectivity across its range. We collected, sequenced, and analyzed tissue samples from 376 individuals from 38 sites, 11 states, and 8 ecoregions using genotyping-by-sequencing (GBS). We used Sanger sequencing to sequence a portion of the mtDNA control region from 472 tissue samples from 42 sites, 12 states, and 8&nbsp..., Please see the published manuscript for a detailed description of the methods., , # Genotyping-by-sequencing SNP Dataset for *Corynorhinus rafinesquii* (CORA) and *Myotis austroriparius* (MYAU)

[https://doi.org/10.5061/dryad.stqjq2c5x](https://doi.org/10.5061/dryad.stqjq2c5x)

These SNP data are from three Illumina sequencing runs of *Corynorhinus rafinesquii* (CORA) and *Myotis austroriparius* (MYAU) tissue samples using genotyping-by-sequencing (GBS). All details of the project and sequencing methods can be found in the published manuscripts. We are publishing two separate manuscripts: one for MYAU and one for CORA.

Publication 1 Title: Range-wide Population Genetic Structure and Genetic Diversity of Southeastern Myotis (*Myotis austroriparius*)

Publication 2 Title: Pending (The CORA manuscript is in preparation. We ask that you please refrain from using the CORA sequences at this time. We will update this once the manuscript has been published.)

## Description of the data and file structure

This is a raw sequencing dataset from three sequencing runs on an Ill...