Genetic Diversity and Structure of the Rare Coastal Herb Swertia noguchiana (Gentianaceae) Across Island Populations

Islands play a key role in plant diversification, often harboring endemic species with limited genetic connectivity to mainland populations. Swertia noguchiana is a rare coastal plant endemic to Japan's Fossa Magna region, found only in part of the Izu Peninsula on mainland Honshu and on three islands of the Izu Islands. To clarify the genetic diversity and structure of this species and inform conservation strategies, population genetic analyses were conducted using multiplexed ISSR genotyping by sequencing (MIG‐seq). A total of 830 SNPs were detected across three populations of S. noguchiana , revealing low genetic diversity and small effective population sizes in all populations. Genetic structure analyses indicated clear divergence among populations, with little evidence of admixture. Demographic analyses suggest divergence between the Izu Peninsula population and the Izu Islands populations, potentially during the postglacial period, followed by a later split between the Izu‐Oshima and Niijima populations, with extremely limited subsequent gene flow; however, these inferences are model‐dependent and should be interpreted with caution. These results indicate substantial genetic differentiation among populations, and estimates of recent migration rates suggest that frequent gene flow is unlikely, although occasional dispersal events cannot be excluded. Interspecific comparisons with S. japonica and S. pseudochinensis indicated that S. noguchiana has particularly low genetic diversity. Despite predominant outcrossing, small population sizes, and habitat fragmentation raise concerns about genetic vulnerability. This study provides insights into the genetic differentiation and potential demographic processes of island populations and highlights the importance of conserving insular endemic species with restricted distributions.