DOI: 10.5061/dryad.76hdr7t7s
title: Data from: Local genetic diversity and structure of Asian black bear, <em>Ursus thibetanus</em>, populations in Nagano, Japan

description: Human–bear conflict is a significant and pressing social issue in Japan.
 Understanding genetic diversity, population structure, and local
 population size of the Asian black bear (Ursus thibetanus) is crucial not
 only for improving ecological and genetic knowledge of the species but
 also for developing effective conservation and management measures. We
 therefore examined sex, mitochondrial (mt) DNA variations, and 12 nuclear
 microsatellite genotypes from hair-derived DNA collected using 35 traps in
 the Kiso region, Nagano Prefecture. After rigorous verification of
 microsatellite genotyping, we identified 30 distinct individuals
 (including seven males and 18 females) within an approximately 48 km2
 area. MtDNA analysis revealed that all the males shared haplotype E01,
 while the females possessed three haplotypes, including E07, which was
 detected in Nagano Prefecture for the first time. E07 has previously been
 reported in the Tohoku region and Toyama Prefecture. While the STRUCTURE
 analysis did not reveal any genetic clusters in nuclear DNA, significant
 spatial genetic structures were identified in both mtDNA and nuclear DNA
 variations. In addition, we found no evidence of a recent bottleneck. This
 study is the first to examine the local genetic structure of the black
 bears in Nagano Prefecture. Although no genetic clusters were detected in
 nuclear DNA, the estimated effective population size was not particularly
 large, underscoring the importance of continued genetic monitoring. These
 new findings obtained in this study can contribute to anticipating
 potential conflict zones and guide management and conservation measures in
 the Kiso region.
description: # Data from: Local genetic diversity and structure of Asian black bear,
 *Ursus thibetanus*, populations in Nagano, Japan Dataset DOI:
 [10.5061/dryad.76hdr7t7s](10.5061/dryad.76hdr7t7s) ## Description of the
 data and file structure Koido_Ursus_sampleinfo.xlsx: This file provides
 information on the sample name, identified sex, trap number, geographic
 coordinates (longitude and latitude), mtDNA haplotypes, and 12 nuclear
 microsatellite genotypes for all 30 identified individuals. ### Files and
 variables #### File: Koido_Ursus_sampleinfo.xlsx **Description:** This
 file contains individual-level genetic and sampling information of Asian
 black bears identified in the Kiso region, Nagano Prefecture, Japan. #####
 Variables * `Samples`– unique identifier for each individual. * `Sex`–
 biological sex of each individual (M = male, F = female, NA =
 undetermined). * `Trap_number` – trap ID (T1–35). * `Latitude` –
 geographic coordinate (decimal degrees, North). * `Longitude` – geographic
 coordinate (decimal degrees, East). * `Haplotype`– mitochondrial DNA
 haplotype code (e.g., E01, E07, E17). Individuals with missing mtDNA data
 are indicated as "NA". * `nSSR_genotypes` – allelic data for 12
 nuclear microsatellite loci. Each locus is represented by two columns,
 corresponding to the two diploid alleles (allele sizes in base pairs).
 Missing alleles are indicated as "NA". **Missing values:**
 indicated as "NA". ## Code/software **Code/software** *
 **Viewing data:** Files are provided in `.xlsx` format, which can be
 opened with Microsoft Excel or other spreadsheet software. * **Analysis
 software:** Genetic analyses were conducted using GenAlEx (version 6.5),
 FSTAT (version 2.9.3), FreeNA, and STRUCTURE v2.3.4. ## Access information
 Other publicly accessible locations of the data: * Access information: Not
 applicable. All data are original to this study.