DOI: 10.5061/dryad.v15dv420g
title: Microsatellite genotypes of Japanese abies species: Insights from population genetics and SDM

description: Range shifts during the Pleistocene shaped the unique phylogeographical
 structures of many species. Pleistocene range shifts gave currently
 allopatric species opportunities to occur in sympatry, likely resulting in
 ancient introgressions between related taxa. In our study, we investigate
 the range shifts and introgression patterns of three Japanese Abies
 species (A. firma, A. homolepis, and A. veitchii) by employing an
 extensive survey of 43 populations. This survey includes comprehensive
 analysis of both mitochondrial (mtDNA) and nuclear (18 microsatellites)
 genomes, in combination with species distribution modeling (SDM). It is
 important to note that these two types of markers provide distinct and
 complementary information, as they have different modes of inheritance and
 mutation rates. Bayesian clustering analysis indicates that the three
 species were clearly separated, with the exception of the A. homolepis
 var. umbellata population, which is considered a natural hybrid between A.
 homolepis and A. firma. However, mtDNA haplotypes of the four northern
 populations of A. firma were entirely replaced by two major haplotypes of
 A. homolepis and A. veitchii. The results of Neighbor-net, NewHybrids,
 STRUCTURE analyses, and SDM suggest that historical introgression between
 species occurred in each geographic region, with mtDNA capture being the
 likely mechanism. However, contrary to these findings, the ABC coalescent
 analysis did not support an ancient introgression. Therefore, further
 validation with genome-wide level data is needed to clarify this issue.
 Our conclusion is that climate-induced range shifts during the
 Pleistocene/Holocene likely played a crucial role in the observed patterns
 of introgression in these species.
description: Multilocus genotypes at 21 microsatellite loci (Abfi13, Abfi18 (Saito et al., 2005), As08, As09, As13
 (Lian et al., 2007), NFF7 and NFH15 (Hansen et al., 2005), c66, c4656,
 c14606, c16096, c32446, c49, c7912, c13359, c14033, c14394, c11017,
 c17556, c28104 and c32410 (Uchiyama et al., 2013).) were
 collected by multiplex PCR and capillary gel electrophoresis. All allele
 calls were scored with GeneMapper 3.7 software.
description: Missing values are coded as 0.
description: # Title of Dataset: Microsatellite Genotypes of Japanese *Abies* Species:
 Insights from Population Genetics and SDM.xlsx --- **GENERAL INFORMATION**
 **Author Information:** Principal Investigator Contact Information Name:
 Kentaro Uchiyama Institution: Department of Molecular Genetics and
 Biotechnology, Forestry and Forest Products Research Institute Address:
 Tsukuba, Ibaraki, 305-8687, Japan Email: kruchiyama@affrc.go.jp Associate
 or Co-investigator Contact Information Name: Yoshihiko Tsumura
 Institution: Faculty of Life and Environmental Sciences, University of
 Tsukuba Address: Tsukuba, Ibaraki 305-8572, Japan Email:
 tsumura.yoshihiko.ke@u.tsukuba.ac.jp **Geographic location of data
 collection**: Japan **Funding Information**: This study was partly
 supported by the JSPS KAKENHI program (grant nos. 21H02240 and 15K07489).
 **SHARING/ACCESS INFORMATION** Links to publications that cite or use the
 data: Uchiyama K, Fujii S, Tsuyama I, Tanaka N, Setsuko S, Kimura MK,
 Suyama Y, Tsumura Y (2023) Range shift and introgression of three Japanese
 *Abies* species: insights from population genetic data and species
 distribution modelling. Tree Genetics & Genomes Links to other
 publicly accessible locations of the data: None Links/relationships to
 ancillary data sets: None Was data derived from another source? No If yes,
 list source(s): NA Recommended citation for this dataset: Uchiyama K,
 Fujii S, Tsuyama I, Tanaka N, Setsuko S, Kimura MK, Suyama Y, Tsumura Y
 (2023) Range shift and introgression of three Japanese Abies species:
 insights from population genetic data and species distribution modelling.
 Dryad Digital Repository. https://doi:10.5061/dryad.v15dv420g ##
 Description of the Data and file structure **File List**: Microsatellite
 Genotypes Data: Contains genotypes determined using specific
 microsatellite loci. Additional related data collected that was not
 included in the current data package: None Are there multiple versions of
 the dataset? No If yes, name of file(s) that was updated: NA Why was the
 file updated? NA When was the file updated? NA DATA-SPECIFIC INFORMATION
 FOR: Microsatellite Genotypes Data Number of variables: 7 (including ID
 and 6 loci) Number of cases/rows: 806 trees from 43 populations
 Description: Samples were collected from 806 trees representing 43
 populations dispersed widely across the natural distribution of three
 Japanese Abies species. The three species included 419 individuals from 22
 populations of A. firma, 153 individuals from nine populations of A.
 homolepis (including one population of A. homolepis var. umbellata), and
 232 individuals from 12 populations of A. veitchii. Multilocus genotypes
 at 21 microsatellite loci were collected by multiplex PCR and capillary
 gel electrophoresis. All allele calls were scored with GeneMapper 3.7
 software. **Variable List**: ID: Individual's ID code. The prefix
 indicates the species (f for Abies firma, h for Abies homolepis, and v for
 Abies veitchii), followed by a three-letter population name. Example:
 fKMG-10 represents an individual from the Abies firma species, from the
 KMG population. Locus Columns (e.g., As09-1, As09-2, etc.): Each locus has
 two columns representing the first and second alleles for that locus. The
 numbers represent the allele sizes. Example: For the individual fKMG-10,
 at the As09 locus, the two alleles are 253 and 267. Missing data codes: 0
 Specialized formats or other abbreviations used: None