Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis

The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone do..., Individuals (N = 267) were collected from 12 Castanopsis species, including: 21 C. carlesii; 25 C. fargesii; 25 C. eyrei; 24 C. lamontii; 28 C. fabri; 19 C. hystrix; 20 C. fordii; 26 C. tibetana; 10 C. chinensis; 23 C. sclerophylla; 24 C. jucunda; and 22 C. fissa (Supplementary Table S1). For each individual, genomic DNA was extracted from silica-dried leaves using a Plant DNA Kit (Bioteke, Beijing, China) and sequenced on the Illumina NovaSeq 6000 platform (150-bp paired-end reads) with a target coverage of 30×.
Raw sequencing data were cleaned using Trimmomatic v.0.38 (Bolger et al. 2014) to remove low quality sequences. Cleaned reads were then aligned to the C. eyrei reference genome using BWA v.0.7.15 (Li and Durbin 2010), and genotypes called using HaplotypeCaller implemented in GATK v.4.1 (Depristo et al. 2011). All individuals included in this study exhibited a high mapping rate (90.26%-98.32%), with a relative low mapping rate appearing to be individual-specific rather than spec..., , # **Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis**

[https://doi.org/10.5061/dryad.kkwh70scm](https://doi.org/10.5061/dryad.kkwh70scm)

We have submitted SNP data (267ind.Chr0.het.again.mac.recode.vcf.gz - 267ind.Chr12.het.again.mac.recode.vcf.gz,)

, chromosome information ([id_conversion.tsv](https://datadryad.org/stash/downloads/file_stream/3295293)) and custom script (script.txt)

1，SNP data

The 13 zip files contain 52,385,983 high-quality single nucleotide polymorphisms (SNPs) called from 267 *Castanopsis* individuals based on whole genome resequencing data. They are in the VCF format, and were generated using the GATK software. Sample information can be found in table S1 in Supplementary Information of the manuscript. For detailed information on how the vcf files were created we refer to the Material and Methods section in the manuscript. The first 12 zipped vcf files (267ind.Chr0.het.again.mac.recode.vcf.gz - 267i...