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<p>Relict and peripheral tree populations may combine reduced within-population variation with strong among-population divergence, complicating conservation decisions. We combined a de novo draft genome assembly of <i>Platycladus orientalis</i> (~ 8.73 Gbp; N50 = 248,484&#xa0;bp) with genotyping-by-sequencing data comprising 38,820 single-nucleotide polymorphisms from 95 individuals in seven Korean stands. Nucleotide diversity was higher in the Danyang–Jecheon limestone corridor (π = 0.245–0.274) than in the isolated Andong, Yeongyang, and Daegu populations (π = 0.156–0.216). The isolated populations were strongly differentiated from one another (pairwise FST = 0.396–0.431), whereas differentiation within the corridor was lower but heterogeneous (FST = 0.117–0.223). Hierarchical analysis of molecular variance attributed 29.26% of variation to differences among populations (ΦST = 0.293). No repeated or near-identical multilocus genotypes were detected. Rarefied private allelic richness among common variants was greater at the corridor-group level than in the isolated group (0.1214 vs. 0.0415 per locus), although rare variants were underestimated. FIS declined strongly under stricter depth and missing-data filters, indicating a substantial technical component in baseline heterozygote deficits. Contemporary effective population size estimates were highly heterogeneous and imprecise, ranging from 2.0 in Danyang Seokmun to 202.8 in Daegu, while Danyang Hasi-ri was unbounded. Exploratory Mantel tests suggested nominal geographic and climatic associations, but none remained significant after multiple-test correction. Adult–seedling FST values were ≤ 0.035 in three focal stands. These results support treating the isolated stands as candidate conservation units and the limestone corridor as a management-relevant diversity reservoir, while gene flow or seed transfer should be evaluated through a risk-assessed framework.</p>

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Genomic structure of relict Platycladus orientalis in Korea reveals isolated lineages and a limestone-corridor diversity hotspot

  • 期刊论文

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  • 发表日期：

    2026年7月11日

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  • Ji Sun Jung,
  • Ji Won Son,
  • Jin Ho Shin,
  • Gwang Gyu Lee

摘要

Relict and peripheral tree populations may combine reduced within-population variation with strong among-population divergence, complicating conservation decisions. We combined a de novo draft genome assembly of Platycladus orientalis (~ 8.73 Gbp; N50 = 248,484 bp) with genotyping-by-sequencing data comprising 38,820 single-nucleotide polymorphisms from 95 individuals in seven Korean stands. Nucleotide diversity was higher in the Danyang–Jecheon limestone corridor (π = 0.245–0.274) than in the isolated Andong, Yeongyang, and Daegu populations (π = 0.156–0.216). The isolated populations were strongly differentiated from one another (pairwise FST = 0.396–0.431), whereas differentiation within the corridor was lower but heterogeneous (FST = 0.117–0.223). Hierarchical analysis of molecular variance attributed 29.26% of variation to differences among populations (ΦST = 0.293). No repeated or near-identical multilocus genotypes were detected. Rarefied private allelic richness among common variants was greater at the corridor-group level than in the isolated group (0.1214 vs. 0.0415 per locus), although rare variants were underestimated. FIS declined strongly under stricter depth and missing-data filters, indicating a substantial technical component in baseline heterozygote deficits. Contemporary effective population size estimates were highly heterogeneous and imprecise, ranging from 2.0 in Danyang Seokmun to 202.8 in Daegu, while Danyang Hasi-ri was unbounded. Exploratory Mantel tests suggested nominal geographic and climatic associations, but none remained significant after multiple-test correction. Adult–seedling FST values were ≤ 0.035 in three focal stands. These results support treating the isolated stands as candidate conservation units and the limestone corridor as a management-relevant diversity reservoir, while gene flow or seed transfer should be evaluated through a risk-assessed framework.