Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)

Abstract

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.

Variability in foraging behaviour of chick-rearing macaroni penguins Eudyptes chrysolophus and its relation to diet

“…Each bird included in the study was sexed by bill measurement following Woehler (1995) and their breast feathers marked Dietary analysis. The dietary data presented here are a subset of those considered in a previous study that examined stomach contents of 69 birds and obtained diet data through genetic analysis of faecal samples (Deagle et al 2007). In the current study, only the stomach content data from birds equipped with data loggers (n = 43) are included, and the individual variation in diet composition is the focus rather than overall diet.…”

“…In addition, dive data have been recorded over the entire annual cycle for some birds from South Georgia (Green et al 2005). The diet of the species has been examined during the breeding season at several colonies and is usually dominated by euphausiids, but fish and other crustaceans can dominate the diet in some years or at some times of the annual cycle (Croxall & Prince 1980, Brown & Klages 1987, Klages et al 1989, Green et al 1998, Barlow et al 2002, Crawford et al 2003, Deagle et al 2007, Cherel et al 2007. No studies on macaroni penguins have related the diet of individual birds to their foraging behaviour.…”

DNA Metabarcoding as a Marine Conservation and Management Tool: A Circumpolar Examination of Fishery Discards in the Diet of Threatened Albatrosses

“…However, in most systems stable isotope analyses lack the resolution to identify prey beyond broad trophic groups. DNA metabarcoding of predator scats is a useful alternate or complementary method for assessing seabird diet (Deagle et al, 2007;Bowser et al, 2013). It can provide highlevel taxonomic resolution and does not require prey remains to be physically identifiable (Pompanon et al, 2012).…”

Opposing Lethal Wildlife Research When Nonlethal Methods Exist: Scientific Whaling as a Case Study

“…Briefly, for example, in early dietary studies involving free-living marine wildlife, lethal sampling often was the simplest method available. However, recent studies involving stomach flushing of sharks (Barnett et al 2010;Hammerschlag and Sulikowski 2011) and elephant seals (Daneri et al 2015), fecal studies of fur seals (GalloReynoso and Esperón-Rodríguez 2013) and penguins (Deagle et al 2007), and stable isotope analysis of sea turtles (Shimada et al 2014) all illustrate how nonlethal methodologies can be made best practice for marine species. In cetacean biology, whale abundance trends and biological parameters can be obtained via boat surveys, land-based observations, and mark-recapture studies.…”