DOI: 10.5061/dryad.stqjq2c5x
title: Genotyping-by-sequencing Single-nucleotide Polymorphism Dataset for Corynorhinus rafinesquii (CORA) and Myotis austroriparius (MYAU)

description: 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 ecoregions. GBS results indicated
 that MYAU has a single, panmictic population with little genetic structure
 and should be managed as so. Results from mtDNA indicated higher
 levels of genetic structure, likely due to low effective
 population size, some level of sex-biased dispersal, and
 increased mutation rates, but not enough to consider separate
 management units or clades. Genetic diversity estimates were low
 to moderate. Results from this study can be used to infer and
 improve long-term protection and management protocols for MYAU.
 Researchers and managers should preserve gene flow and ensure
 subpopulations remain connected by maintaining forest corridors and
 protecting natural and artificial roosts for MYAU in order to
 prevent future population segregation.
description: Please see the published manuscript for a detailed description of
 the methods.
description: # 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 Illumina Nextseq 500. This is the original dataset with no editing or filtering. This dataset was later edited and filtered for downstream analyses so if you wish to use this dataset, you may want to consider the following. Here are notes on samples that were edited or removed in downstream analyses for various reasons: Samples 0811_02 and 0811_03 are duplicated as 0811-02 and 0811-03, respectively, and did not combine because of the underscore versus the dash in the name. 0811_02 and 0811-02 are the same samples. This is the same for 0811_03 and 0811-03 as well. Samples 1102_01 and 1102_02 also have the wrong site number. It should be site 75 for both (not site 74). If site does not matter, then this will not affect anything. I removed sample NC_E7 because of unknown location and uncertainty on species. It is very likely MYAU, but the collector did not label properly. AR_D5 was removed because we later found out that this was a different species (misidentified by the collector). I also removed samples from sites 48, 49, and 50 because the species names were mixed up. All samples collected at sites 48, 49, and 50 are CORA, although samples R32, R44, P71, P73, I1, I2, I3, I4, and I5 were mistakenly labelled as MYAU. Those samples can be used as CORA samples, not MYAU (even though the label says MYAU). For reference, the site numbers are at the end of the file names. If you would like specific data on sites, please reach out to the primary author. For MYAU, I removed site 73 (sample A68, which is the only sample from that site) because all loci had "NA", so it was uncertain why it was ever retained. I later determined it was CORA rather than MYAU as originally labeled. For CORA, I removed the single sample from Georgia because it was the only one collected in that state. I also removed one SNP (TP756944) that was not genotyped in Texas. Sample CORA_OK_351 was removed because it is likely a misidentified species (misidentified by collector). I have also included a keyfile with barcodes for each sample across all three sequencing runs. Each full sample name includes the species (MYAU or CORA), the state abbreviation (United States), the unique alphanumeric sample code (created by the authors), and the site number (assigned by the authors), in that order. Each sequencing run contains 4 files, which each correspond to 1 of 4 lanes used during the sequencing run. Sequencing run AH27M2BGX9 (see Flowcell column in the keyfile) is named "undetermined" in the uploaded files. The other two sequencing runs are AH52MHBGX5 and AHYLLJBGX5. ## Sharing/Access information If you have specific questions about the dataset, such as requests for more specific metadata, please reach out to the corresponding author. ## Code/Software Please see the manuscript for a description of software used.