| Summary: | Humpback whales, Megaptera novaeangliae, from the southern hemisphere undergo large scale seasonal migrations between their summer feeding grounds near Antarctica and their winter reproductive grounds in the subtropical to tropical regions. However, population structure data in the southern hemisphere is scarce. The aim of this study was to get information on stocks structure in the Southern hemisphere using chemical tracers; stable isotopes and persistent organic pollutants (POPs) concentrations in Humpback whales from two stocks: stock C1 breeding off Mozambique and stock G breeding off Ecuador. Material and methods: Skin and blubber biopsies of humpback whales from Ecuador (2014-2015, n= 60) and Mozambique (2017, n=89) were sampled. δ13C and δ15N values were analyzed in skin. POPs were analyzed in the blubber: polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and organochlorine pesticides (OCPs) including dichlorodiphenyltrichloroethane and its metabolites (DDXs), hexachlorobenzene (HCB), lindane (HCHs), chlordanes (CHLs) and methoxylated PBDEs (MeO-PBDEs). Gender was determined genetically (see Das et al. 2017 for detail in methodology). Results: Low δ13C and δ15N values in skin reflected their diet focused mainly on low trophic level prey species, such as krill from Antarctica, Euphausia superba. One group in the Mozambique stock had higher δ15N values. Gender did not account for this variation. Other driving factors could be the metabolic state, the age, the geographic δ15N variations in feeding grounds, or a more opportunistic diet in Antarctica that includes small fish. The isotopic niches from Mozambique and Ecuador did not overlap indicating that the two populations exploit different resources. The differences in δ13C (p-value < 0.01) between the two populations suggested a different geographic source of primary productivity meaning the whales do not feed in the same area. However, female humpback whales in Ecuador had significant lower δ15N (p-value < 0.01) and δ13C ...
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