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BackgroundDetermination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches.Methodology/Principal FindingsPrey-specific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (crèche) stage. These trends followed those observed in the penguins' stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented.Conclusions/SignificanceThe present study is one of the first to examine the full breadth of a predator's diet using DNA-based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds.

A ntarctic krill Euphausia superba, a key species in Southern Ocean food webs 1 , plays a central role in ecosystem processes and community dynamics of apex predators, and is the target of a commercial fishery 2 . Krill spawn in late spring and their larvae develop during summer, autumn and under the ice in winter to emerge as juveniles in the following spring. The newly spawned eggs sink from the surface to up to 1,000 m depth where they hatch and the developing larvae actively swim upwards to feed in the upper water column 1 . Larval Antarctic krill have low lipid reserves, which are insufficient to support long periods of starvation. Therefore, winter, when primary production is minimal, is assumed to be a critical bottleneck for larval krill development and hence recruitment to the adult population 3,4 . Present hypotheses suggest that high algal biomass in winter sea ice enhances larval krill winter-feeding conditions and growth [5][6][7][8] . This implies that larvae have access to this high algal biomass within the sea ice. However, recent observations 9,10 indicate that the linkage between sea ice and krill recruitment success is not as direct as has been suggested. The timing of ice-edge advance and annual ice-season duration is highly variable, and does not necessarily show a clear link to krill recruitment in the following year ( Supplementary Figs. 1 and 2). Along the Antarctic Peninsula, adult krill have a five to six year population cycle with oscillations in biomass exceeding an order of magnitude 9 . According to bioenergetics models, part of the variability is due to interannual variation in reproductive output 11 as well as autumn blooms that may govern the possible overwinter survival rate of larvae 11,12 . In the Bransfield Strait, three krill winter surveys have shown that krill abundance is an order of magnitude higher than in summer, regardless of concurrent sea-ice conditions 10 A dominant Antarctic ecological paradigm suggests that winter sea ice is generally the main feeding ground for krill larvae. Observations from our winter cruise to the southwest Atlantic sector of the Southern Ocean contradict this view and present the first evidence that the pack-ice zone is a food-poor habitat for larval development. In contrast, the more open marginal ice zone provides a more favourable food environment for high larval krill growth rates. We found that complex under-ice habitats are, however, vital for larval krill when water column productivity is limited by light, by providing structures that offer protection from predators and to collect organic material released from the ice. The larvae feed on this sparse ice-associated food during the day. After sunset, they migrate into the water below the ice (upper 20 m) and drift away from the ice areas where they have previously fed. Model analyses indicate that this behaviour increases both food uptake in a patchy food environment and the likelihood of overwinter transport to areas where feeding conditions are more favourable in spring.