Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale ( Megaptera novaeangliae ) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3575 samples spanning the seven breeding stocks and...

Often abundance of rare species cannot be estimated with conventional design‐based methods, so we illustrate with a population of blue whales ( Balaenoptera musculus ) a spatial model‐based method to estimate abundance. We analyzed data from line‐transect surveys of blue whales off the coast of Chile, where the population was hunted to low levels. Field protocols allowed deviation from planned track lines to collect identifica...