Molecular diet analysis of two african free-tailed bats (molossidae) using high throughput sequencing

Abstract

Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5' tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated.

Figure 1. The overall distribution of unique sequences determined in pellets from Chaerephon pumilus (n = 59), and Mops condylurus (n = 30).

The column ‘artefacts’ refers to sequences that could not be assigned to Insecta.

Figure 2. Frequency of occurrence (percent of pellets) of insect orders (with assigned families) in the diet of Chaerephon pumilus (n = 59) and Mops condylurus (n = 30).

Figure 3. Prey accumulation curve (Colwell 2005) for prey insect families identified in the faeces of Chaerephon pumilus and Mops condylurus.

Number of pellets corresponds to sampling intensity.

Figure 4. Distribution of MOTUs among pellets.

Figure 5. Diversity indices based on resampling of MOTUs.

(Fig. 5a) Shannon Index, (Fig. 5b) Simpson Index.