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<p><i>Eriocaulon nudicuspe</i> is a threatened plant species distributed at discrete seepage wetlands in Central Honshu, Japan. These wetlands have been present over a million years and functioned as refugia during the glacial periods. The species is an endemic of the wetland ecosystems, but its natural habitats are fragmented by land development. We aimed to identify the genetic structure and diversity of <i>E. nudicuspe</i> and to assess the implications for conservation. We performed Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) and selected 2349 SNPs that were genotyped in 102 individuals from 14 natural and 2 human-established populations. Genetic population structure analyses identified four genetic groups: eastern, northern central, southern central, and western. Demographic modelling suggested that first three groups (eastern, central, and western) simultaneously diverged in prehistoric times, followed by the central group diverging into northern and southern groups. Observed heterozygosity was lower in the populations at the edge of the species’ distribution than in the others, probably due to foundation effects associated with the limitation of suitable habitats. The human-established populations had similar genetic diversity and composition to those of the geographically closest natural populations, indicating a low risk of outbreeding depression or genetic bottleneck. We propose four major conservation units, which can be useful for the development of strategies for ex-situ conservation and genetic management of restoration. Although conservation of remnant natural populations should be prioritized, establishing new populations with adequate genetic management seems an effective option to restore connectivity between wetlands isolated by urbanization.</p>

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Conservation genetics of the threatened wetland plant Eriocaulon nudicuspe: application of GRAS-Di sequencing technology and implications for restoration

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  • 发表日期：

    2025年5月30日

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  • Ikuyo Saeki,
  • Akira S. Hirao

摘要

Eriocaulon nudicuspe is a threatened plant species distributed at discrete seepage wetlands in Central Honshu, Japan. These wetlands have been present over a million years and functioned as refugia during the glacial periods. The species is an endemic of the wetland ecosystems, but its natural habitats are fragmented by land development. We aimed to identify the genetic structure and diversity of E. nudicuspe and to assess the implications for conservation. We performed Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) and selected 2349 SNPs that were genotyped in 102 individuals from 14 natural and 2 human-established populations. Genetic population structure analyses identified four genetic groups: eastern, northern central, southern central, and western. Demographic modelling suggested that first three groups (eastern, central, and western) simultaneously diverged in prehistoric times, followed by the central group diverging into northern and southern groups. Observed heterozygosity was lower in the populations at the edge of the species’ distribution than in the others, probably due to foundation effects associated with the limitation of suitable habitats. The human-established populations had similar genetic diversity and composition to those of the geographically closest natural populations, indicating a low risk of outbreeding depression or genetic bottleneck. We propose four major conservation units, which can be useful for the development of strategies for ex-situ conservation and genetic management of restoration. Although conservation of remnant natural populations should be prioritized, establishing new populations with adequate genetic management seems an effective option to restore connectivity between wetlands isolated by urbanization.