The description of trophic interactions and food webs is a funda‐ mental process in understanding ecosystems functionality (Krahn et al., 2007; Symondson, 2002). Multiple ecological‐informed manage‐ ment decisions rely on dietary studies, such as the trophic position of species and their demographic regulation, based on the impor‐ tance of feeding resources, or the impact of species interactions (e.g., predation) on populations and communities (e.g., Alonso et al., 2014). Moreover, predator–prey interactions define most of the food web dynamics (Carreon‐Martinez & Heath 2010; Jo, Gim, Jeong, Kim, & Joo, 2014), and given the current environmental changing scenario, their better knowledge is necessary to design effective management and conservation plans (Bradley et al., 2007; Roslin & Majaneva, 2016). Traditionally, species' diets have been mostly identified through direct observation of predatory events or by visual mor‐ phological analysis of stomach, gut, or fecal contents (Caryl et al., 2012; Reñones, Polunin, & Goni, 2002). The accuracy of such Received: 5 June 2019 | Revised: 10 July 2019 | Accepted: 12 July 2019 DOI: 10.1002/edn3.27

https://onlinelibrary.wiley.com/doi/pdf/10.1002/edn3.27

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and ...

The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite!

DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.

/pdf/dna-barcoding-a-unique-avifauna-an-important-tool-for-37gxicebok.pdf

DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation

The growing grey seal (Halichoerus grypus) population in the Baltic Sea has created conflicts with local fisheries, comparable to similar emerging problems worldwide. Adequate information on the foraging habits is a requirement for responsible management of the seal population. We investigated the applicability of available dietary assessment methods by comparing morphological analysis and DNA metabarcoding of gut contents (short-term diet; n = 129/125 seals, respectively), and tissue chemical markers i.e. fatty acid (FA) profiles of blubber and stable isotopes (SIs) of liver and muscle (mid- or long-term diet; n = 108 seals for the FA and SI markers). The methods provided complementary information. Short-term methods indicated prey species and revealed dietary differences between age groups and areas but for limited time period. In the central Baltic, herring was the main prey, while in the Gulf of Finland percid and cyprinid species together comprised the largest part of the diet. Perch was also an important prey in the western Baltic Proper. The DNA analysis provided firm identification of many prey species, which were neglected or identified only at species group level by morphological analysis. Liver SIs distinguished spatial foraging patterns and identified potentially migrated individuals, whereas blubber FAs distinguished individuals frequently utilizing certain types of prey. Tissue chemical markers of adult males suggested specialized feeding to certain areas and prey, which suggest that these individuals are especially prone to cause economic losses for fisheries. We recommend combined analyses of gut contents and tissue chemical markers as dietary monitoring methodology of aquatic top predators to support an optimal ecosystem-based management.

/pdf/complementary-methods-assessing-short-and-long-term-prey-of-56k3khalrr.pdf

Complementary methods assessing short and long-term prey of a marine top predator - Application to the grey seal-fishery conflict in the Baltic Sea

Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.We used stable isotopes, morphological, and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.

Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free-ranging consumers.

In recent decades, grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena) have become more numerous along the coasts of Brittany in northwestern France. Their interactions with fisheries are of increasing concern and diet analyses are becoming a requirement to determine the actual overlap between species targeted by fisheries and marine mammal prey. However, as only a few stranded or by-caught animals are available to investigate the diet of these top predators, it is necessary to optimize the results obtained from each animal sampled by increasing the rate of prey species determination in stomach contents. We used a combined analysis of stomach contents, based on prey hard remains and, in parallel, a simple DNA barcoding approach to identify the soft remains. Seven grey seal stomachs and three harbour porpoise stomachs have been analysed. The combined approach, making use of visual observation as well as DNA analysis, increased the identification of prey items by around 32% for...

DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena)

In recent decades, grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena) have become more numerous along the coasts of Brittany in northwestern France. Their interactions with fisheries are of increasing concern and diet 15 analyses are becoming a requirement to determine the actual overlap between species targeted by fisheries and marine mammal prey. However, as only a few stranded or by-caught animals are available to investigate the diet of these top predators, it is necessary to optimize the results obtained from each animal sampled, by increasing the rate of prey species determination in stomach contents. We used a combined analysis of stomach contents, based on prey hard remains and, in parallel, a simple DNA barcoding approach to identify the soft remains. Seven grey seal stomachs and three harbour 20 porpoise stomachs have been analysed. The combined approach, making use of visual observation as well as DNA analysis, increased the identification of prey items by around 32% for grey seal and by 21% for harbour porpoise. Fish species identified include Mediterranean and Atlantic horse mackerel (Trachurus mediterraneus and Trachurus trachurus), Atlantic mackerel (Scomber scombrus), ballan and cuckoo wrasse (Labrus bergylta and Labrus mixtus), European seabass (Dicentrarchus labrax), Atlantic pollock (Pollachius pollachius), European conger (Conger conger) and garfish (Belone belone). One fish species 25 (L. bergylta) was identified only with DNA methods. An area-specific diet for the grey seal in the Iroise Sea, proposed by others in a previous study, seems to be supported.

DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour

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DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour porpoises (Phocoena phocoena)

DNA barcoding for the identification of soft remains of prey in the stomach contents of grey seals (Halichoerus grypus) and harbour