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Aziz SA, Clements GR, Peng LY, Campos-Arceiz A, McConkey KR, Forget PAA, Gan HM.2016. Elucidating the diet and foraging ecology of the island flying fox (Pteropus hypomelanus) in Peninsular Malaysia through Illumina Next-Generation Sequencing. PeerJ Preprints4:e2547v1https://doi.org/10.7287/peerj.preprints.2547v1
There is an urgent need to identify and understand the ecosystem services provided by threatened animal species such as flying foxes. The first step towards this is to obtain comprehensive data on their diet. However, the volant and nocturnal nature of flying foxes presents a challenging situation, and conventional microhistological approaches to studying their diet can be laborious and time-consuming, and provide incomplete information. We used Illumina Next-Generation Sequencing (NGS) as a novel, non-invasive method for analysing the diet of the island flying fox (Pteropus hypomelanus) on Tioman Island, Peninsular Malaysia. Through NGS analysis of flying fox droppings over eight months, we identified at least 29 Operationally Taxonomic Units comprising the diet of this giant pteropodid, spanning 19 genera and 18 different plant families, including one new family not previously recorded for pteropodid diet. NGS was just as successful as conventional microhistological analysis in detecting plant taxa from droppings, but also uncovered six additional plant taxa. The island flying fox’s diet appeared to be dominated by figs (Ficus sp.), which was the most abundant plant taxon detected in the droppings every single month. Our study has shown that NGS can add value to the conventional microhistological approach in identifying food plant species from flying fox droppings. However, accurate and detailed identification requires a comprehensive database of the relevant plant DNA, which may require collection of botanical specimens from the study site. Although this method cannot be used to quantify true abundance or proportion of plant species, nor plant parts consumed, it ultimately provides a very important first step towards identifying plant taxa in pteropodid diet.
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Raw data of proportion of OTU reads detected in flying fox droppings across 8 months (Mar-Oct 2015) at 2 different roosting sites on Tioman, Juara (J) and Tekek (T)
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