DOI: 10.5061/dryad.6q573n64h
title: Data from: Divergent mechanisms of reduced growth performance in Betula ermanii saplings from high-altitude and low-latitude range edges

description: 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.
description: # 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.