Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric “ecotypes” with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from ∼150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.

Summary 1.The social structure of a population plays a key role in many aspects of its ecology and biology. It influences its genetic make-up, the way diseases spread through it and the way animals exploit their environment. However, the description of social structure in nonprimate animals is receiving little attention because of the difficulty in abstracting social structure from the description of association patterns between individuals. 2. Here we focus on recently developed analytical techniques that facilitate inference about social structure from association patterns. We apply them to the population of bottlenose dolphins residing along the Scottish east coast, to detect the presence of communities within this population and infer its social structure from the temporal variation in association patterns between individuals. 3. Using network analytical techniques, we show that the population is composed of two social units with restricted interactions. These two units seem to be related to known differences in the ranging pattern of individuals. By examining social structuring at different spatial scales, we confirm that the identification of these two units is the result of genuine social affiliation and is not an artefact of their spatial distribution. 4. We also show that the structure of this fission-fusion society relies principally on short-term casual acquaintances lasting a few days with a smaller proportion of associations lasting several years. These findings highlight how network analyses can be used to detect and understand the forces driving social organization of bottlenose dolphins and other social species.

Determining management units for natural populations is critical for effective conservation and management. However, collecting the requisite tissue samples for population genetic analyses remains the primary limiting factor for a number of marine species. The harbour porpoise (Phocoena phocoena), one of the smallest cetaceans in the Northern Hemisphere, is a primary example. These elusive, highly mobile small animals confound traditional approaches of collecting tissue samples for genetic analyses, yet their nearshore habitat makes them highly vulnerable to fisheries by-catch and the effects of habitat degradation. By exploiting the naturally shed cellular material in seawater and the power of next-generation sequencing, we develop a novel approach for generating population-specific mitochondrial sequence data from environmental DNA (eDNA) using surface seawater samples. Indications of significant genetic differentiation within a currently recognized management stock highlights the need for dedicated eDNA sampling throughout the population's range in southeast Alaska. This indirect sampling tactic for characterizing stock structure of small and endangered marine mammals has the potential to revolutionize population assessment for otherwise inaccessible marine taxa.

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Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioural and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350 000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the last glacial maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including interoceanic and interhemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirms genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification.

Taxonomy is an imprecise science that delimits the evolutionary continuum into discrete categories. For marine mammals, this science is complicated by the relative lack of morphological data for taxa that inhabit remote and often vast ranges. We provide guidelines to promote consistency in studies relying primarily on molecular genetic data to delimit cetacean subspecies from both populations and species. These guidelines identify informational needs: basis for the taxonomic hypothesis being tested, description of current taxonomy, description of relevant life history, sample distribution, sample size, number and sequence length of genetic markers, description of measures taken to ensure data quality, summary statistics for the genetic markers, and analytical methods used to evaluate the genetic data. We propose an initial set of quantitative and qualitative standards based on the types of data and analytical methods most readily available at present. These standards are not expected to be rigidly applied. Rather, they are meant to encourage taxonomic arguments that are consistent and transparent. We hope professional societies, such as the Society for Marine Mammalogy, will adopt quantitative standards that evolve as new data types and analytical methods become widely available.

The Southern Resident killer whale population (Orcinus orca) was listed as endangered in 2005 and shows little sign of recovery. These fish eating whales feed primarily on endangered Chinook salmon. Population growth is constrained by low offspring production for the number of reproductive females in the population. Lack of prey, increased toxins and vessel disturbance have been listed as potential causes of the whale’s decline, but partitioning these pressures has been difficult. We validated and applied temporal measures of progesterone and testosterone metabolites to assess occurrence, stage and health of pregnancy from genotyped killer whale feces collected using detection dogs. Thyroid and glucocorticoid hormone metabolites were measured from these same samples to assess physiological stress. These methods enabled us to assess pregnancy occurrence and failure as well as how pregnancy success was temporally impacted by nutritional and other stressors, between 2008 and 2014. Up to 69% of all detectable pregnancies were unsuccessful; of these, up to 33% failed relatively late in gestation or immediately post-partum, when the cost is especially high. Low availability of Chinook salmon appears to be an important stressor among these fish-eating whales as well as a significant cause of late pregnancy failure, including unobserved perinatal loss. However, release of lipophilic toxicants during fat metabolism in the nutritionally deprived animals may also provide a contributor to these cumulative effects. Results point to the importance of promoting Chinook salmon recovery to enhance population growth of Southern Resident killer whales. The physiological measures used in this study can also be used to monitor the success of actions aimed at promoting adaptive management of this important apex predator to the Pacific Northwest.

Social network correlates of food availability in an endangered Social network correlates of food availability in an endangered population of killer whales, Social network correlates of food availability in an endangered population of killer whales, Orcinus orca