A biopsy consists of removing a small sample of tissue from a living animal for examination. In the framework of marine mammal research, biopsies of skin and blubber can provide a large amount of information. In whales, biopsies are generally collected using a crossbow and hollow-tipped arrow. The system is designed so that the arrow pops out of the animal tissue once it has reached the blubber layer, and floats to allow samplers to collect it at the surface. Biopsies in pinnipeds are performed using a manual punch while animals are under anesthesia.

As all types of tissues are primarily made off cells containing the DNA of the individual, skin samples can be used for genetic studies on marine mammals, to study stock structure, social relationships and evolutionary history.

Skin samples can also be used for the analysis of biochemical trophic markers, particularly carbon and nitrogen stable isotope ratios. The isotopic ratios are reliable indicators of the foraging ecology of a species. The relative abundance of δ13C provides information on the source of primary production underlying the food chain. It therefore allows the differentiation between species feeding on benthic versus pelagic organisms. Meanwhile, the relative abundance of δ15N increases systematically according to the trophic level of an organism. Therefore, the δ15N signature of a predator is greater than that of its prey. Marine mammal diet can also be examined using fatty acid signature analysis. Adipose tissue (fat) is mostly constituted of lipids, which contain fatty acids. Fatty acids often deposit in adipose tissue with very little modification. Since species can only produce a limited number of different fatty acid chains, analysis of the fatty acid composition of an organism can determine the species which constitutes its diet.

Fat tissues are also useful in ecotoxicology studies. Unlike water-soluble molecules which are eliminated from organisms through the blood circulation, fat-soluble contaminants deposit in adipose tissues where they accumulate. Persistent organic pollutants (POPs) are fat-soluble contaminants that are resistant to biological degradation and bio-accumulate in food chains. Because marine mammals are often top predators in their ecosystem, POP levels in their adipose tissues are particularly important. Analysis of the content of marine mammal adipose tissues can therefore serve as indicators of the pollution level of their habitat and help unravel the effects of diverse chemicals on the species' health and ecology.

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