Data from: Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges
Data files
Oct 05, 2023 version files 487.33 MB
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README.md
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vcfAfterFiltering.tar.gz
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vcfAfterLDPruning.tar.gz
Abstract
The reduced growth performance of individuals from range edges is a common phenomenon in various taxa, and considered to be an evolutionary factor that limits the species’ range. However, most studies did not distinguish between two mechanisms that can lead to this reduction: genetic load and adaptive selection to harsh conditions. This study investigated the climatic and genetic factors underlying the growth performance of Betula ermanii saplings transplanted from 11 populations including high-altitude edge and low-latitude edge population using RAD-seq analysis.
For 11 B. ermanii populations in wide-latitude range of Japan, we estimated gene diversity, nucleotide diversity, the coefficients of linkage disequilibrium, genetic differentiation between populations, population structure as well as the relatedness coefficient from SNPs. As a result, the low-latitude edge population exhibited a high level of linkage disequilibrium, low genetic diversity, a distinct genetic composition from the other populations, and a high relatedness coefficient.
This data contains two SNPs datas (vcf files) used in these analysis. We analyzed SNPs data separately for 8 planting sites. Then each tarball contains 8 separate vcf files. One tarball named "vcfAfterFiltering" contains vcf files after SNP filtering steps used for the calculation of the coefficients of linkage disequilibrium. Another tarball named "vcfAfterLDPruning" contains vcf files after SNP filtering and before LD-based pruning used for the calculation of other genetic parameters.
README: Title of Dataset
Data from: Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges
GENERAL INFORMATION
Author Information:
Principal Investigator Contact Information
Name: Takaki Aihara
Institution: Graduate School of Life and Environmental Sciences, University of Tsukuba
Address: 1-1-1, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
Email: aiharatk4@gmail.com
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 supported by the JSPS KAKENHI program (grant no. 21H04732) and the JST Challenging Research Program for Next Generation Researchers (grant no. JPMJSP2124).
SHARING/ACCESS INFORMATION
Links to publications that cite or use the data:
Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y (2023) Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Heredity
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:
Aihara T, Araki K, Onuma Y, Cai Y, Paing AMM, Goto S, Hisamoto Y, Tomaru N, Homma K, Takagi M, Yoshida T, Iio A, Nagamatsu D, Kobayashi H, Hirota M, Uchiyama K, Tsumura Y (2023) Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges. Dryad Digital Repository. https://doi:10.5061/dryad.v15dv420g
Description of the data and file structure
This data contains two tarballs containing vcf files used in these analysis. We analyzed SNPs data separately for 8 planting sites. Then each tarball contains 8 separate vcf files.
File List:
vcfAfterFiltering.tar.gz: Contains vcf files of each planting site' set after SNP filtering. SNPsAfterFiltering(Name of planting site). This data used for the calculation of the coefficients of linkage disequilibrium.
vcfAfterLDPruning.tar.gz: Contains vcf files of each planting site' set after SNP filtering and LD-based pruning. SNPsAfterLDPruning(Name of planting site). This data used for the calculation of other genetic parameters.