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Identifying prey of the Javan mongoose (Urva javanica) in Java from fecal samples using next-generation sequencing

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Abstract

The Javan mongoose (Urva javanica) is a mesopredator native to Java island that has been rarely studied. The limited information raises questions as to its ecological roles, particularly in terms of its effects on agriculture and biodiversity. These questions are critical as its congeneric species, the small Indian mongoose, has been listed among the 100 worst invasive species. To disclose its ecological function, a new approach that is capable of revealing the diet of the Javan mongoose at the species level is required. We conducted this study to identify the prey species of the Javan mongoose using next-generation sequencing methodology. Our study was conducted in a forested area of the southern mountains of Java, Indonesia. We collected fecal samples during the dry season of March–October 2018, extracting DNA using a QIAamp Fast DNA Stool Mini Kit. We performed Illumina sequencing using a 133 bp mini-barcode of the Cytochrome Oxidase I gene. Our rigorous analysis found 17 species, 14 genera, and 12 families of vertebrates and invertebrates in the mongoose feces. The greater bandicoot rat (Bandicota indica) and the domestic chicken (Gallus gallus) made up the primary diet of the Javan mongoose. Cricket, ant, moth, and fly species were also found in the feces. In effect, our results suggested that this species has a relatively diverse diet, one that includes mammals, birds, amphibians, snakes, fish, and many invertebrates. It confirms that the Javan mongoose has an opportunistic diet, which is most likely related to the availability of putative prey.

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(Redrawn from Veron and Jennings 2017)

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References

  • Ando H, Fujii C, Kawanabe M, Ao Y, Inoue T, Takenaka A (2018) Evaluation of plant contamination in metabarcoding diet analysis of a herbivore. Sci Rep 8:2–11. https://doi.org/10.1038/s41598-018-32845-w

    Article  CAS  Google Scholar 

  • André A, Millien V, Galan M, Ribas A, Michaux JR (2017) Effects of parasite and historic driven selection on the diversity and structure of a MHC-II gene in a small mammal species (Peromyscus leucopus) undergoing range expansion. Evol Ecol 31:785–801

    Article  Google Scholar 

  • Andriollo T, Gillet F, Michaux JR, Ruedi M (2019) The menu varies with metabarcoding practices: a case study with the bat Plecotus auritus. PLoS ONE 14(7):e0219135. https://doi.org/10.1371/journal.pone.0219135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beng KC, Tomlinson KW, Shen XH, Surget-Groba Y, Hughes AC, Corlett RT, Slik JWF (2016) The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics. Sci Rep 6:1–13. https://doi.org/10.1038/srep24965

    Article  CAS  Google Scholar 

  • Biffi M, Laffaille P, Jabiol J, André A, Gillet F, Lamothe S, Michaux JR, Buisson L (2017) Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods. Mamm Biol 87:176–184. https://doi.org/10.1016/j.mambio.2017.09.001

    Article  Google Scholar 

  • Casper RM, Jarman SN, Deagle BE, Gales NJ, Hindell MA (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. J Exp Mar Bio Ecol. https://doi.org/10.1016/j.jembe.2007.04.002

    Article  Google Scholar 

  • Devloo-Delva F, Huerlimann R, Chua G, Matley JK, Heupel MR, Simpfendorfer CA, Maes GE (2018) How does the marker choice affect your diet analysis? Comparing genetic markers and digestion levels in metabarcoding of reef predator gut content. Mar Freshw Res 70:8–18

    Article  Google Scholar 

  • Edgar R (2010) Usearch. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA, USA

  • Elbardicy S, Tadros M, Yousif F, Hafez S (2009) Predatory activity of Psychoda alternata (Diptera: Psychodidae) larvae on Biomphalaria glabrata and Lymnaea natalensis snails and the free-living larval stages of Schistosoma mansoni. Aust J Basic Appl Sci 3:4503–4509

    Google Scholar 

  • ElEla SA, ElSayed W, Nakamura K (2013) Mandibular structure, gut contents analysis and feeding group of orthopteran species collected from different habitats of Satoyama area within Kanazawa City, Japan. J Threat Taxa 02:849–857. https://doi.org/10.11609/jott.o2346.849-57

    Article  Google Scholar 

  • Gillet F, Tiouchichine ML, Galan M, Blanc F, Némoz M, Aulagnier S, Michaux JR (2015) A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces. Mamm Biol 80:505–509. https://doi.org/10.1016/j.mambio.2015.08.002

    Article  Google Scholar 

  • Gorman ML (1975) The diet of feral Herpestes auropunctatus (Carnivora: Viverridae) in the Fijian Islands. J Zool 175:273–278. https://doi.org/10.1111/j.1469-7998.1975.tb01401.x

    Article  Google Scholar 

  • Hebert PDN, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci 101:14812–14817

    Article  CAS  Google Scholar 

  • Hinton HE (1956) The larvae of the species of Tinidae of economic importance. Bull Entomol Res 47:251–346

    Article  Google Scholar 

  • Kalle R, Ramesh T, Qureshi Q, Sankar K (2012) Diet of mongoose in Mudumalai Tiger Reserve, southern India. Sci Trans Environ Technovation 6:44–51

    Google Scholar 

  • Karremans AP, Pupulin F, Grimaldi D, Beentjes KK, Butôt R, Fazzi GE, Kaspers K, Kruizinga J, Roessingh P, Smets EF, Gravendeel B (2015) Pollination of Specklinia by nectar-feeding Drosophila: the first reported case of a deceptive syndrome employing aggregation pheromones in Orchidaceae. Ann Bot 116:437–455. https://doi.org/10.1093/aob/mcv086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurahashi H, Benjapong N, Omar B (1997) Blow flies (Insecta: Diptera: Calliphoridae) of Malaysia and Singapore. Raffles Bull Zool 5:1–88

    Google Scholar 

  • Litvaitis JA, Pearl MC (2000) Investigating food habits of terrestrial vertebrates. In: Boitani L, Fuller TK (eds) Research techniques in animal ecology. Columbia University Press, New York, pp 165–190

    Google Scholar 

  • Macías-Hernández N, Athey K, Tonzo V, Wangensteen OS, Arnedo M, Harwood JD (2018) Molecular gut content analysis of different spider body parts. PLoS ONE 13:e0196589

    Article  Google Scholar 

  • Mahmood T, Adil A (2017) Diet composition of small Indian mongoose (Herpestes javanicus) varies seasonally in its native range. Anim Biol 67:69–80. https://doi.org/10.1163/15707563-00002516

    Article  Google Scholar 

  • Marquina D, Andersson AF, Ronquist F (2019) New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour 19:90–104. https://doi.org/10.1111/1755-0998.12942

    Article  CAS  PubMed  Google Scholar 

  • Monterroso P et al (2019) Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysis. Mamm Rev 49(2):97–112

    Article  Google Scholar 

  • Mumma MA, Adams JR, Zieminski C, Fuller TK, Mahoney SP, Waits LP (2016) A comparison of morphological and molecular diet analyses of predator scats. J Mammal 97:112–120. https://doi.org/10.1093/jmammal/gyv160

    Article  Google Scholar 

  • Ratnasingham S, Hebert PDN (2007) The barcode of life data system (www.barcodinglife.org). Mol Ecol Notes 7:355–364. https://doi.org/10.1111/j.1471-8286.2006.01678.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robinson MH, Pratt T (1975) The phenology of Hexacentrus mundus (F. Walker) at Wau, Papua New Guinea (Orthoptera, Tettigoniidae). Psyche J Entomol 82:3–4. https://doi.org/10.1134/s0374064117080118

    Article  Google Scholar 

  • Seaman GA, Randall JE (1962) The mongoose as a predator in the Virgin Islands. J Mammal 43:544–546

    Article  Google Scholar 

  • Shehzad W, Mccarthy TM, Pompanon F, Purevjav L, Riaz T, Taberlet P (2012) Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia. PLoS ONE 7:1–8. https://doi.org/10.5061/dryad.bj376f61

    Article  Google Scholar 

  • Taberlet P, Bonin A, Coissac E, Zinger L (2018) Environmental DNA: for biodiversity research and monitoring. Oxford University Press, Oxford

    Book  Google Scholar 

  • Turbanova AA, Turbanov IS, Gorbunov OG (2019) To the knowledge of the biology and distribution of Monopis crocicapitella (Clemens, 1860) (Lepidoptera: Tineidae), with remarks on cavernicolous Lepidoptera. Russ Entomol J 28:72–81. https://doi.org/10.15298/rusentj.28.1.12

    Article  Google Scholar 

  • Veron G, Jennings AP (2017) Javan mongoose or small Indian mongoose–who is where? Mamm Biol 87:62–70

    Article  Google Scholar 

  • Veron G, Patou M-L, Pothet G, Simberloff D, Jennings AP (2007) Systematic status and biogeography of the Javan and small Indian mongooses (Herpestidae, Carnivora). Zool Scr 36:1–10

    Article  Google Scholar 

  • Way M, Khoo KC (1992) Role of ants in pest management. Annu Rev Entomol 37:479–503. https://doi.org/10.1146/annurev.ento.37.1.479

    Article  Google Scholar 

  • Zeale MRK, Butlin RK, Barker GLA, Lees DC, Jones G (2011) Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol Ecol Resour 11:236–244. https://doi.org/10.1111/j.1755-0998.2010.02920.x

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We are grateful for a research grant awarded from Universitas Gadjah Mada and the Ministry of Research, Technology, and Higher Education of Indonesia (research contract no. 64/UN1/DITLIT/DIT-LIT/LT/2018), which enabled us to conduct this study.

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Authors and Affiliations

  1. Faculty of Forestry, Universitas Gadjah Mada, Jl. Agro No. 1. Bulaksumur, Yogyakarta, 55281, Indonesia

    Sena A. Subrata

  2. Universitas Atmajaya Yogyakarta, Jl. Babarsari No. 44, Babarsari, Yogyakarta, 55281, Indonesia

    Stefanie R. T. Siregar

  3. Conservation Genetics Unit, Department of Life Sciences, University of Liège, 4000, Liege, Belgium

    Adrien André & Johan R. Michaux

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  1. Sena A. Subrata
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  2. Stefanie R. T. Siregar
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  3. Adrien André
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  4. Johan R. Michaux
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Correspondence to Sena A. Subrata.

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Subrata, S.A., Siregar, S.R.T., André, A. et al. Identifying prey of the Javan mongoose (Urva javanica) in Java from fecal samples using next-generation sequencing. Mamm Biol 101, 63–70 (2021). https://doi.org/10.1007/s42991-020-00086-y

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