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Abstract RationaleStable isotope analysis (SIA) of free‐swimming mysticetes using biopsies is often limited in sample size and uses only one sample per individual, failing to capture both intra‐individual variability and the influence of demographic and physiological factors on isotope ratios. MethodsWe applied SIA of δ¹³C and δ¹⁵N to humpback whale (Megaptera novaeangliae) biopsies taken during the foraging season along the western Antarctic Peninsula to quantify intra‐individual variation from repeatedly sampled individuals, as well as to determine the effect of biopsy collection site, sex, and pregnancy on isotope ratios. ResultsThere was substantial variability in δ¹³C from multiple biopsies taken from the same individuals, though δ¹⁵N was much more consistent. Side of the body (left versus right) and biopsy location (dorsal, anterior, ventral, and posterior) did marginally affect the isotopic composition of δ¹⁵N but not δ¹³C. Pregnancy had a significant effect on both δ¹³C and δ¹⁵N, where pregnant females were depleted in both when compared to non‐pregnant females and males. ConclusionsThese results indicate that isotopic signatures are influenced by multiple endogenous and exogenous factors and emphasize value in accounting for intra‐individual variability and pregnancy status within a sampled population. Placed within an ecological context, the endogenous variability in δ¹³C observed here may be informative for future isotopic analyses. 

Abstract Southern hemisphere blue (Balaenoptera musculus intermedia) and fin (Balaenoptera physalus) whales are the largest predators in the Southern Ocean, with similarities in morphology and distribution. Yet, understanding of their life history and foraging is limited due to current low abundances and limited ecological data. To address these gaps, historic Antarctic blue (n = 5) and fin (n = 5) whale baleen plates, collected in 1947–1948 and recently rediscovered in the Smithsonian National Museum of Natural History, were analyzed for bulk (δ¹³C and δ¹⁵N) stable isotopes. Regular oscillations in isotopic ratios, interpreted as annual cycles, revealed that baleen plates contain approximately 6 years (14.35 ± 1.20 cm year⁻¹) of life history data in blue whales and 4 years (16.52 ± 1.86 cm year⁻¹) in fin whales. Isotopic results suggest that: (1) while in the Southern Ocean, blue and fin whales likely fed at the same trophic level but demonstrated niche differentiation; (2) fin whales appear to have had more regular annual migrations; and (3) fin whales may have migrated to ecologically distinct sub‐Antarctic waters annually while some blue whales may have resided year‐round in the Southern Ocean. These results reveal differences in ecological niche and life history strategies between Antarctic blue and fin whales during a time period when their populations were more abundant than today, and before major human‐driven climatic changes occurred in the Southern Ocean.