Microsatellite genotypes of Japanese abies species: Insights from population genetics and SDM
Data files
Sep 06, 2023 version files 152.49 KB
Abstract
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.
README: 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
Methods
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.
Usage notes
Missing values are coded as 0.