Population genomics reveals demographic history and climate adaptation in Japanese Arabidopsis halleri

Climate oscillations in the Quaternary forced species to major latitudinal or altitudinal range shifts. It has been suggested that adaptation concomitant with range shifts plays key roles in species responses during climate oscillations, but the role of selection for local adaptation to climatic changes remains largely unexplored. Here, we investigated population structure, demographic history, and signatures of climate-driven selection based on genome-wide polymorphism data of 141 Japanese Arabidopsis halleri individuals, with European ones as outgroups. Coalescent-based analyses suggested a genetic differentiation between Japanese subpopulations since the Last Glacial Period (LGP), which would have contributed to shaping the current pattern of population structure. Population demographic analysis revealed the population size fluctuations in the LGP, which were particularly prominent since the subpopulations started to diverge (~50 kya). The ecological niche modeling predicted the geog..., We used whole genome re-sequencing data of Japanese (141 individuals from 135 populations) and European (12 individuals from 10 Central European populations and 4 individuals from 4 Romanian populations) Arabidopsis halleri individuals. Our analysis includes population structure analysis using non-negative matrix factorization (sNMF) (Frichot et al., 2014; Frichot and François, 2015), genome-wide association mapping for bioclimatic variables using latent factor mixed models (LFMM) (Caye et al., 2019; Gain and François, 2021), genome-wide selection scans based on cross-population extended haplotype homozygosity (XP-EHH) (Gautier et al., 2017), and enrichment analysis of the climate-associated loci in the extreme tails of selection scans with permutation test using the “genome rotation” scheme (Atwell et al., 2010; Horton et al., 2012; Nordborg et al., 2005; Sasaki et al., 2022; Tsuchimatsu et al., 2020)., , # Population genomics reveals demographic history and climate adaptation in Japanese Arabidopsis halleri

[https://doi.org/10.5061/dryad.1jwstqk3s](https://doi.org/10.5061/dryad.1jwstqk3s)

This dataset includes input SNP data and source code used in analysis of genetic differentiation and climate adaptation in Japanese *Arabidopsis halleri*.

We obtained re-sequencing data of Japanese (141 individuals) and European(12 Central European and 4 Romanian individuals) *A. halleri*. We mapped short reads to the *A. halleri* v2.03 assembly (DOE-JGI, [http://phytozome.jgi.doe.gov/](http://phytozome.jgi.doe.gov/)) using BWA-MEM 0.7.17-r1188 (Li, 2013), and bcftools v.1.17 mpileup and call (Danecek et al., 2021) pipeline.

## Description of the data and file structure

#### SNP data

##### Ah\_JP\_EU.Q20.MAF005.DP15004300.FM01.vcf.gz

* SNP data for Japanese and European individuals.
* SNPs with quality ≤ 20, minor allele frequency ≤ 0.05, total depth ≤ 1,500 or total depth ≥ 4,300, and a fracti...