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Conservation genetics of three Rafflesia species in Java Island, Indonesia using SNP markers obtained from MIG-seq

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Rafflesia species (Rafflesiaceae) are among the flagship plants of South-East Asian countries in which they occur. Three species of Rafflesia, i.e. Rafflesia patma, R. rochussenii, and R. zollingeriana, are known from Java, Indonesia. All three species are threatened with extinction due to human activities that cause habitat loss and fragmentation. Conservation efforts such as determining conservation units for prioritization of those species have been difficult due to the lack of data on their population genetics. Availability of genetic information is important to develop appropriate conservation measures. Our study evaluates genetic diversity and structure of the three Rafflesia species using a total of 166 samples across the island. We used single nucleotide polymorphism (SNP) markers obtained via MIG-seq. The three species of Rafflesia in Java bear much lower genetic diversity compared to what was previously shown for R. speciosa and R. lagascae on Borneo, the Philippines and the Malayan Peninsula. Low genetic diversity within the Javanese Rafflesia species, particularly in R. patma and R. zollingeriana, is attributed to bottleneck events and population expansion in the past. We also provide evidence of clonality and existence of different genotypes within Tetrastigma host plants in two species of Rafflesia. Scattered and fragmented populations as reconstructed in the genetic structure analyses are important to be considered in designing appropriate conservation strategies. Furthermore, we demonstrate how the establishment of Rafflesia ex-situ collections can conserve genetic diversity that may no longer be present in nature and could be used in future reintroduction programs.

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The datasets generated and analyzed during the current study are available on the OSF repository (


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The authors are very grateful to the director and staff of all conservation areas where the fieldwork was conducted. A special thanks goes to Dewi Lestari for her help doing the survey. A particular thanks goes also to Ruliyana Susanti (Research Center for Biology–LIPI), Fajria Novary (Ministry of Environment and Forestry of the Republic of Indonesia) and Hendra Helmanto (Bogor Botanic Gardens–LIPI) for their help to obtain the permits. We also sincerely thank the local people who assisted the field work across Java (Cagar Alam and Taman Nasional). The support by the Leonardo-Office Saxony team (TU Dresden) for facilitating the administration needed to complete the ERASMUS+ mobilities is very much appreciated.


This study was supported by Japan Science and Technology Agency (JST), Collaboration Hubs for International Research Program (CHIRP) within the framework of the Strategic International Collaborative Research Program (SICORP), and Environmental Research & Technology Development Fund (Grant Nos. 4-1902 & 4-1605). ERASMUS+funding was granted to TU Dresden to support mobilities between institutions.

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YWCK and YI: developed and designed the research. YWCK: conducted the fieldwork and sample collection. YWCK, AM, and YS: run the laboratory works. YWCK, AM, and YS: performed the SNP calling and data analyses. YWCK, SW and YI: wrote the manuscript. YWCK: is the main contributor. All authors have read and approved the final manuscript.

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Correspondence to Yayan Wahyu Candra Kusuma.

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Kusuma, Y.W.C., Matsuo, A., Suyama, Y. et al. Conservation genetics of three Rafflesia species in Java Island, Indonesia using SNP markers obtained from MIG-seq. Conserv Genet 23, 1039–1052 (2022).

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