DOI: 10.5061/dryad.kkwh70scm
title: Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis

description: 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 does not fully explain the observed patterns of genomic
 variation; the effects of recurrent selective sweeps must be
 considered. We further revealed that extensive gene flow has
 significantly influenced patterns of genomic variation in Castanopsis
 species. The estimated admixture proportion correlated positively with
 recombination rate and negatively with gene density, supporting a scenario
 of selection against gene flow. Additionally, putative introgression
 regions exhibited strong signals of positive selection, an enrichment of
 functional genes, and reduced genetic burdens, indicating that adaptive
 introgression has played a role in shaping the genomes of hybridizing
 species. This study provides insights into how different evolutionary
 forces have interacted in driving the evolution of the genomic variation
 landscape.
description: Individuals (<em>N</em> = 267) were collected from 12
 <em>Castanopsis</em> species, including: 21 <em>C.
 carlesii</em>; 25 <em>C. fargesii</em>; 25 <em>C.
 eyrei</em>; 24 <em>C. lamontii</em>; 28 <em>C.
 fabri</em>; 19 <em>C. hystrix</em>; 20 <em>C.
 fordii</em>; 26 <em>C. tibetana</em>; 10 <em>C.
 chinensis</em>; 23 <em>C. sclerophylla</em>; 24
 <em>C. jucunda</em>; and 22 <em>C. fissa
 </em>(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 <em>C. eyrei</em> 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
 species-specific (Supplementary Table S1 and Fig S20), suggesting that
 there is no species-specific bias due to divergence from the reference.
 These results suggested that the effects of reference bias were likely
 minimal in this study. To further minimize bias in SNP and genotype
 calling, SNPs that met any of the following conditions were discarded: (1)
 located within repetitive regions of the <em>C. eyrei</em>
 reference genome; (2) more than two alleles present; (3) sequencing depth
 &gt; 100 or &lt; 5; (4) missing rate ≥ 0.3; (4) heterozygosity
 rate (proportion of heterozygotes among all genotypes) &gt; 0.5; (6)
 indels. Additionally, only homozygous genotypes supported by ≥ 4 reads
 were considered. For heterozygous genotypes, the minor allele was required
 to be supported by ≥ 2 reads, and the read ratio (number of reads
 supporting the minor allele/the number of reads supporting the major
 allele) was required to be &gt; 0.1 and &lt; 0.9.
description: # **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 - 267ind.Chr11.het.again.mac.recode.vcf.gz) contain SNPs called from the chromosomes 1-12, respectively. The 13th zipped vcf file (267ind.Chr12.het.again.mac.recode.vcf.gz) contain SNPs called from all other scaffolds that did not mapped to the 12 chromosomes. 2，chromsome information (id_conversion.tsv) The 12 chromosomes were arranged based on their respective length, when presenting figures and tables in the manuscript. This file serves to provide information regarding the chromosome numbers in the VCF files with those referenced in the manuscript. 3, custom script (script.txt) Custom scripts (Python and Bash) used for data analyses in this study. The reference genome and short read sequences have been deposited in Genbank (under the accession number: PRJNA1097334 and PRJNA1097337) and NGDC (under accession number: PRJCA026947 and PRJCA026948).