Data from: Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

DNA-based techniques have proven useful for defining trophic links in a variety of ecosystems and recently developed sequencing technologies provide new opportunities for dietary studies. We investigated the diet of Australian fur seals (Arctocephalus pusillus doriferus) by pyrosequencing prey DNA from faeces collected at three breeding colonies across the seals’ range. DNA from 270 faecal samples was amplified with four polymerase chain reaction primer sets and a blocking primer was used to limit amplification of fur seal DNA. Pooled amplicons from each colony were sequenced using the Roche GS-FLX platform, generating > 20 000 sequences. Software was developed to sort and group similar sequences. A total of 54 bony fish, 4 cartilaginous fish and 4 cephalopods were identified based on the most taxonomically informative amplicons sequenced (mitochondrial 16S). The prevalence of sequences from redbait (Emmelichthys nitidus) and jack mackerel (Trachurus declivis) confirm the importance of these species in the seals’ diet. A third fish species, blue mackerel (Scomber australasicus), may be a more important prey species than previously recognised. There were major differences in the proportions of prey DNA recovered in faeces from different colonies, probably reflecting differences in prey availability. Parallel hard-part analysis identified largely the same main prey species as did the DNA-based technique, but with lower species diversity and no remains from cartilaginous prey. The pyrosequencing approach presented significantly expands the capabilities of DNA-based methods of dietary analysis and is suitable for large-scale diet investigations on a broad range of animals.

基于DNA的技术已被证实可有效解析多种生态系统中的营养联系，而近年发展的测序技术则为饮食生态学研究提供了全新契机。本研究通过焦磷酸测序（pyrosequencing）技术，对澳大利亚海狗（*Arctocephalus pusillus doriferus*）的食性展开探究：采集该物种活动范围内3个繁殖种群的粪便样本，对其中的猎物DNA进行分析。本研究使用4组聚合酶链式反应（polymerase chain reaction，PCR）引物对270份粪便样本中的DNA进行扩增，并通过阻断引物（blocking primer）抑制海狗自身DNA的扩增；将每个繁殖种群的扩增产物混合后，依托罗氏GS-FLX测序平台进行测序，共获得超过20000条序列读段。本研究开发了专用软件，用于对相似序列进行分类与聚类。基于测序获得的最具分类学信息量的扩增片段（线粒体16S，mitochondrial 16S），本研究共鉴定出54种硬骨鱼、4种软骨鱼以及4种头足类动物。红饵鱼（*Emmelichthys nitidus*）与澳洲竹荚鱼（*Trachurus declivis*）的序列占比，证实了这两个物种在海狗食性中的重要地位。第三种鱼类——澳洲鲭（*Scomber australasicus*），其作为猎物的重要性或远超此前认知。不同繁殖种群粪便样本中检出的猎物DNA占比存在显著差异，这大概率反映了不同海域的猎物可获得性差异。平行开展的硬组织分析结果与DNA测序技术鉴定出的主要猎物物种大体一致，但物种多样性更低，且未检出软骨鱼类的残骸。本研究采用的焦磷酸测序方法，大幅拓展了基于DNA的食性分析技术的应用能力，适用于多种动物的大规模食性调查研究。