Biogeographical Distribution Model of Flowering Plant Capparis micracantha Using Support Vector Machine (SVM) and Generalized Linear Model (GLM) and its Ex-situ Conservation Efforts

Inggit Puji Astuti, Angga Yudaputra, Dipta Sumeru Rinandio, Ade Yusuf Yuswandi


Capparis micracantha is a flowering plant species with a wide range of distributions. It is often used as traditional medicine by local people. This species is often overlooked due to very limited information that reveals about its conservation aspects. This study aims to update the distribution records and predict the potential current distribution of this species. Some new occurrence records were obtained through a direct field survey, plant inventory database, and reliable scientific papers. In order to gain more information about current distribution, Species Distribution Modelling (SDM) was applied to predict the potential current distribution of this species in Indonesia.  Two algorithms of machine learning (SVM and GLM) were applied to produce predictive distribution maps. The models were built from occurrence records data and environmental variables (climate and topography). Area Under Curve (AUC) was used to evaluate the model prediction. The AUC value of those models >0.80 means those models have a good performance. The AUC value of those models is stated in SVM (0.86) and GLM (0.824). SVM and GLM have almost similar resulting predictive maps of current distribution. The predictive maps would be useful to give information about the regions in Indonesia that have similar environment characteristics and climate conditions where the species are observably present. This species has also been conserved through ex-situ conservation strategies, but the seedling growth of this species still remains a challenge.


Biogeographical distribution; Capparis micracantha; Ex-situ conservation; GLM; SVM.

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D. J. Mabberley, Mabberley’s plant-book: a portable dictionaryof plants, their classification and uses. England: Cambridge University Press, 2008.

M. Jacobs, “The genus Capparis (Capparaceae) from the Indus to the Pacific,†Blumea - Biodiversity, Evol. Biogeogr. Plants, vol. 12, no. 3, pp. 385–541, 1964.

D. T. Sy et al., “Capparis kbangensis (Capparaceae), a new species from central Vietnam,†PhytoKeys, vol. 151, pp. 83–91, 2020.

M. A. R. Batuyong, M. A. Calaramo, and G. J. D. Alejandro, “A checklist and conservation status of vascular plants in the Limestone forest of Metropolitan Ilocos Norte Watershed Forest Reserve, Northwestern Luzon, Philippines,†Biodiversitas, vol. 21, no. 9, pp. 3969–3981, 2020.

M. Jacobs, “Capparidaceae,†in Flora Malesiana, Series I Spermatophyta, Volume 6, C. G. G. J. van Steenis, Ed. Djakarta: Noordhoff-Kolff, 1960, pp. 61–105.

W. Widodo and M. J. Luthfi, “Checklist of flowering plants (Magnoliophyta) of mount Nglanggeran, Gunungkidul: confirmation and update of Flora of Java and APG III,†Biol. Med. Nat. Prod. Chem., vol. 6, no. 1, pp. 19–36, 2017.

Y. W. N. Ratnaningrum, S. Indrioko, E. Faridah, and A. Syahbudin, “View of Gene flow and selection evidence of sandalwood (Santalum album) under various population structures in Gunung Sewu (Java, Indonesia), and its effects on genetic differentiation,†Biodiversitas, vol. 18, no. 4, pp. 1493–1505, 2017.

Y. W. N. Ratnaningrum and A. Kurniawan, “View of Floral structure and genetical differences of sandalwood variants in Gunung Sewu (Java, Indonesia), and its effects on breeding systems and reproductive ability,†Biodiversitas, vol. 20, no. 2, pp. 393–404, 2019.

J. B. Kim and D. H. Bae, “Intensification characteristics of hydroclimatic extremes in the Asian monsoon region under 1.5 and 2.0°C of global warming,†Hydrol. Earth Syst. Sci., vol. 24, no. 12, pp. 5799–5820, Dec. 2020.

G. U. Stuart, “Salimbagat / Capparis micracantha DC,†List of Philipine herbal medicine plant, 2018. [Online]. Available: [Accessed: 25-May-2021].

O. Neamsuvan, P. Komonhiran, and K. Boonming, “Medicinal plants used for hypertension treatment by folk healers in Songkhla province, Thailand,†J. Ethnopharmacol., vol. 214, pp. 58–70, Mar. 2018.

F. I. Windardi, “Capparis micracantha DC,†in Plant Resources of South-East Asia No 12 (2): Medicinal and poisonous plants 2, J. L. C. H. Van Valkenburg and N. Bunyapraphatsara, Eds. Netherlands: Backhuys Publisher, 2001, p. 140.

K. C. Chinsembu, “Diabetes mellitus and nature’s pharmacy of putative antidiabetic plants,†J. Herb. Med., vol. 15, p. 100230, Mar. 2019.

P. Somwong and C. Chuchote, “Determination of Lupeol, a Cytotoxic Compound Against SW620 Cells in the Extracts of Ha-Rak Recipe,†Pharmacogn. J., vol. 13, no. 1, pp. 133–141, 2021.

J. Lohakul et al., “The protective effect of polyherbal formulation, Harak Formula, on UVA-induced photoaging of human dermal fibroblasts and mouse skin via promoting Nrf2-regulated antioxidant defense,†Front. Pharmacol., vol. 12, p. 649820, Apr. 2021.

C. N. Johnson et al., “Biodiversity losses and conservation responses in the Anthropocene,†Science (80-. )., vol. 356, no. 6335, pp. 270–275, Apr. 2017.

W. J. Ripple, C. Wolf, T. M. Newsome, M. Hoffmann, A. J. Wirsing, and D. J. McCauley, “Extinction risk is most acute for the world’s largest and smallest vertebrates,†Proc. Natl. Acad. Sci. U. S. A., vol. 114, no. 40, pp. 10678–10683, Oct. 2017.

A. Qin et al., “Maxent modeling for predicting impacts of climate change on the potential distribution of Thuja sutchuenensis Franch., an extremely endangered conifer from southwestern China,†Glob. Ecol. Conserv., vol. 10, pp. 139–146, Apr. 2017.

J. C. Deb, S. Phinn, N. Butt, and C. A. McAlpine, “The impact of climate change on the distribution of two threatened Dipterocarp trees,†Ecol. Evol., vol. 7, no. 7, pp. 2238–2248, Apr. 2017.

A. Norberg et al., “A comprehensive evaluation of predictive performance of 33 species distribution models at species and community levels,†Ecol. Monogr., vol. 89, no. 3, p. 1370, Aug. 2019.

E. Kaky, V. Nolan, A. Alatawi, and F. Gilbert, “A comparison between Ensemble and MaxEnt species distribution modelling approaches for conservation: A case study with Egyptian medicinal plants,†Ecol. Inform., vol. 60, p. 101150, Nov. 2020.

M. Abdelaal, M. Fois, G. Fenu, and G. Bacchetta, “Using MaxEnt modeling to predict the potential distribution of the endemic plant Rosa arabica Crép. in Egypt,†Ecol. Inform., vol. 50, pp. 68–75, Mar. 2019.

K. Zhang et al., “Impact of climate factors on future distributions of Paeonia ostii across China estimated by MaxEnt,†Ecol. Inform., vol. 50, pp. 62–67, Mar. 2019.

N. Xu, F. Meng, G. Zhou, Y. Li, B. Wang, and H. Lu, “Assessing the suitable cultivation areas for Scutellaria baicalensis in China using the Maxent model and multiple linear regression,†Biochem. Syst. Ecol., vol. 90, p. 104052, Jun. 2020.

L. Marshall et al., “The interplay of climate and land use change affects the distribution of EU bumblebees,†Glob. Chang. Biol., vol. 24, no. 1, pp. 101–116, Jan. 2018.

M. S. Hosseinzadeh, F. Q. Masood, N. Babak, R. Dennis, and S. M. Kazemi, “Habitat suitability and modelling the potential distribution of the Plateau Snake Skink Ophiomorus nuchalis (Sauria scincidae) on the Iranian Plateau,†North. West. J. Zool., vol. 14, no. 1, pp. 60–63, 2018.

A. Yudaputra, I. P. Astuti, and W. P. Cropper, “Comparing six different species distribution models with several subsets of environmental variables: Predicting the potential current distribution of Guettarda speciosa in Indonesia,†Biodiversitas J. Biol. Divers., vol. 20, no. 8, pp. 2321–2328, Jul. 2019.

A. Yudaputra, “Modelling potential current distribution and future dispersal of an invasive species Calliandra calothyrsus in Bali Island, Indonesia,†Biodiversitas J. Biol. Divers., vol. 21, no. 2, pp. 674–682, Jan. 2020.

D. A. Pisner and D. M. Schnyer, “Support vector machine,†in Machine Learning: Methods and Applications to Brain Disorders, Elsevier, 2019, pp. 101–121.

J. M. Kass, S. I. Meenan, N. Tinoco, S. F. Burneo, and R. P. Anderson, “Improving area of occupancy estimates for parapatric species using distribution models and support vector machines,†Ecol. Appl., vol. 31, no. 1, p. e02228, Jan. 2021.

A. Yudaputra, I. Fijridiyanto, and W. P. Cropper, “The potential impact of climate change on the distribution pattern of Eusideroxylon zwageri (Bornean Ironwood) in Kalimantan, Indonesia,†Biodiversitas, vol. 21, no. 1, pp. 326–333, 2020.

F. Ghareghan, G. Ghanbarian, H. R. Pourghasemi, and R. Safaeian, “Prediction of habitat suitability of Morina persica L. species using artificial intelligence techniques,†Ecol. Indic., vol. 112, p. 106096, May 2020.

O. Ovaskainen et al., “How to make more out of community data? A conceptual framework and its implementation as models and software,†Ecol. Lett., vol. 20, no. 5, pp. 561–576, May 2017.

F. K. C. Hui, “Boral: Bayesian ordination and regression analysis,†R package version 1.4, 2017. [Online]. Available: [Accessed: 25-May-2021].

A. Gayen and H. R. Pourghasemi, “Spatial modeling of gully erosion: A new ensemble of CART and GLM data-mining algorithms,†in Spatial Modeling in GIS and R for Earth and Environmental Sciences, Elsevier, 2019, pp. 653–669.

T. Connor et al., “Effects of grain size and niche breadth on species distribution modeling,†Ecography (Cop.)., vol. 41, no. 8, pp. 1270–1282, Aug. 2018.

T. H. Booth, H. A. Nix, J. R. Busby, and M. F. Hutchinson, “Bioclim: The first species distribution modelling package, its early applications and relevance to most current MaxEnt studies,†Divers. Distrib., vol. 20, no. 1, pp. 1–9, Jan. 2014.

S. E. Fick and R. J. Hijmans, “WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas,†Int. J. Climatol., vol. 37, no. 12, pp. 4302–4315, Oct. 2017.

R. J. Hijmans, S. Phillips, J. Leathwick, and J. Elith, “Dismo: Species distribution modeling,†R Package Version 1.3-3., 2020. [Online]. Available: [Accessed: 24-May-2021].

J. C. Cooper and J. Soberón, “Creating individual accessible area hypotheses improves stacked species distribution model performance,†Glob. Ecol. Biogeogr., vol. 27, no. 1, pp. 156–165, Jan. 2018.

W. J. Krzanowski and D. J. Hand, ROC : Curves for continuous data. Boca Raton, FL: Chapman and Hall/CRC, 2009.

T. Handayani, “Diversity, potential and conservation of Annonaceae in Bogor Botanic Gardens, Indonesia,†Biodiversitas, vol. 19, no. 2, pp. 591–603, 2018.

J. E. Teysmann, Catalogus plantarum quae in Horto Botanico Bogoriensi coluntur. Batavia: Lands-Drukkerij, 1866.

D. Setyanti and D. O. Pribadi, “Mapping the dynamics of dead trees collection to support sustainable landscape management at Bogor Botanic Gardens,†in IOP Conference Series: Earth and Environmental Science, 2020, pp. 1–6.

D. A. Lestari, R. Azrianingsih, and H. Hendrian, “Taxonomical position of Annonaceae species from East Java, Indonesia: Collections of Purwodadi botanic garden based on morphological character,†Biodiversitas, vol. 18, no. 3, pp. 1067–1076, Jul. 2017.

D. A. Lestari, A. P. Fiqa, and I. K. Abywijaya, “Leaf morphological traits of Orophea spp. (Annonaceae): Living collections of Purwodadi Botanic Gardens, East Java, Indonesia,†Biodiversitas J. Biol. Divers., vol. 22, no. 6, pp. 3403–3411, Jun. 2021.

T. Handayani, Yuzammi, and J. T. Hadiah, “Inflorescence morphology and development of Suweg (Amorphophallus paeoniifolius (Dennst.) Nicolson,†Biodiversitas, vol. 21, no. 12, pp. 5835–5844, Dec. 2020.

F. Damayanti, R. Vitri Garvita, H. Wawangningrum, and S. Rahayu, “Flower development, pollen viability and pollen storage test of Aeschynanthus radicans,†Biodiversitas, vol. 22, no. 4, pp. 1940–1945, Apr. 2021.

D. A. Lestari and A. P. Fiqa, “Environmental factors influence on flowering and fruiting period of selected essential oil plants from annonaceae,†Biodiversitas, vol. 21, no. 3, pp. 910–921, Mar. 2020.

B. Moungsrimuangdee, P. Waiboonya, P. Larpkern, P. Yodsa-Nga, and M. Saeyang, “Reproductive phenology and growth of riparian species along Phra Prong river, Sa Kaeo province, Eastern Thailand,†J. Landsc. Ecol., vol. 10, no. 2, pp. 35–48, 2017.



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