Meredith Thornton

Population structure of humpback whales from their breeding grounds in the South Atlantic and Indian oceans

Although humpback whales are among the best-studied of the large whales, population boundaries in the Southern Hemisphere (SH) have remained largely untested. We assess population structure of SH humpback whales using 1,527 samples collected from whales at fourteen sampling sites within the Southwestern and Southeastern Atlantic, the Southwestern Indian Ocean, and Northern Indian Ocean (Breeding Stocks A, B, C and X, respectively). Evaluation of mtDNA population structure and migration rates was carried out under different statistical frameworks. Using all genetic evidence, the results suggest significant degrees of population structure between all ocean basins, with the Southwestern and Northern Indian Ocean most differentiated from each other. Effective migration rates were highest between the Southeastern Atlantic and the Southwestern Indian Ocean, followed by rates within the Southeastern Atlantic, and the lowest between the Southwestern and Northern Indian Ocean. At finer scales, very low gene flow was detected between the two neighbouring sub-regions in the Southeastern Atlantic, compared to high gene flow for whales within the Southwestern Indian Ocean. Our genetic results support the current management designations proposed by the International Whaling Commission of Breeding Stocks A, B, C, and X as four strongly structured populations. The population structure patterns found in this study are likely to have been influenced by a combination of long-term maternally directed fidelity of migratory destinations, along with other ecological and oceanographic features in the region.

Killer Whale Nuclear Genome and mtDNA Reveal Widespread Population Bottleneck during the Last Glacial Maximum

Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline.

RANGE AND MOVEMENTS OF FEMALE HEAVISIDE'S DOLPHINS (CEPHALORHYNCHUS HEAVISIDII), AS DETERMINED BY SATELLITE-LINKED TELEMETRY

Abstract Heavisides dolphin (Cephalorhynchus heavisidii) is a coastal delphinid with a limited inshore distribution off the west coast of southern Africa. Knowledge of its habitat usage is an essential precursor to assessing its potential vulnerability to fisheries interactions. Six Heavisides dolphins (1 male and 5 females) were fitted with satellite-linked transmitters in 2004, and tracked for up to 54 days. The 5 tags fitted to female dolphins transmitted continuously, allowing for analysis of movements at a fine temporal scale. Four dolphins showed an initial avoidance of the capture site by moving over a wider area in the first 2–5 days posttagging than later in the deployment period. All dolphins had used their full home ranges (determined as 100% minimum convex polygons) 5–20 days before tag failure, suggesting measured home ranges were stable at this temporal scale. Home-range estimates using local convex hulls ranged from 301.9 to 1,027.6 km2 (90% isopleths) and 875.9 to 1,989.6 km2 using the 100% isopleths and scaled positively with body size but varied in shape, usage, and number of core-use areas. Although the distance from shore and depth at which individual dolphins moved varied greatly, all dolphins showed a strong onshore–offshore diurnal movement pattern, generally being closest inshore between 0600 h and noon, and farthest offshore between 1500 h and 0500 h. This pattern is assumed to be related to the movements of their principal prey, juvenile shallow-water hake (Merluccius capensis), which migrate into the upper water column at night. Movements inshore may be associated with rest, socializing, and predator avoidance.

Migration redefined? Seasonality, movements and group composition of humpback whales Megaptera novaeangliae off the west coast of South Africa

The migration of Southern Hemisphere humpback whales Megaptera novaeangliae between their feeding and breeding areas has thus far been considered a highly predictable and seasonal event. However, previous observations on the humpbacks that pass through the nearshore waters of the west coast of South Africa have revealed deviations from the behaviour and seasonality expected during a typical migration. This ‘anomaly’ is hypothesised to be associated with prey availability in the region. Shore-based observations between July 2001 and February 2003 from North Head, Saldanha Bay, in the Western Cape province, yielded relative abundances that again did not support a classical migration pattern, with the highest sighting rates from mid-spring through summer. Movement parameters (actual swimming speed, direction and linearity) of humpback groups tracked by theodolite showed mid-spring to be a turning point in their behaviour, after which we observed a significant reduction in actual swimming speed, an increase in ‘non-directional’ movement, and a distribution farther from shore than in other seasons. Additional data on group composition and sex collected between 1993 and 2008 showed a significantly female-biased sex ratio during mid-spring, the first such recorded for any region. Direct observation of feeding on crustacean prey during spring and summer further supports the notion that humpbacks may have more flexible foraging habits than previously appreciated, and that the southern Benguela upwelling region may function as an important feeding area for these whales.

Transit station or destination? Attendance patterns, movements and abundance estimate of humpback whales off west South Africa from photographic and genotypic matching

Humpback whales Megaptera novaeangliae found off west South Africa (WSA) are known to display an atypical migration that may include temporary residency and feeding during spring and summer. At a regional scale there is uncertainty about how these whales relate to the greater West African Breeding Stock B as a whole, with evidence both for and against its division into two substocks. A database containing sighting information of humpback whales intercepted by boat in the WSA region from 1983 to 2008 was compiled. It included a total of 1 820 identification images of ventral tail flukes and lateral views of dorsal fins. After systematic within- and between-year matching of images of usable quality, it yielded 154 different individuals identified by tail flukes (TF), 230 by left dorsal fins (LDF), and 237 by right dorsal fins (RDF). Microsatellite (MS) matching of 216 skin biopsies yielded 156 individuals. By linking all possible sightings of the same individuals using all available identification features, the periodicity and seasonality of 281 individual whales were examined. In all, 60 whales were resighted on different days of which 44 were between different calendar years. The most resightings for one individual was 11 times, seen in six different years, and the longest interval between first and last sightings was about 18 years. A resighting rate of 15.6% of whales at intervals of a year or more indicates long-term fidelity to the region. Shorter intervals of 1–6 months between sequential sightings in the same year may suggest temporary residency. The TF image collection from WSA was compared to TF collections from four other regions, namely Gabon, Cabinda (Angola), Namibia and the Antarctic Humpback Whale Catalogue (AHWC). Three matches were detected between WSA (in late spring or summer) and Gabon (in winter), confirming direct movement between these regions. The capture–recapture data of four different identification features (TF, RDF, LDF and MS) from six successive subsets of data from periods with the highest collection effort (2001–2007) were used to calculate the number of whales that utilise the region, using both closed- and open-population models. Dorsal fins have never been used to estimate abundance for humpback whales, so the different identification features were evaluated for potential biases. This revealed 9–14% incidence of missed matches (false negatives) when using dorsal fins that would result in an overestimate, whereas variation in individual fluke-up behaviour may lower estimates by as much as 57–66% due to heterogeneity of individual capture probability. Taking into consideration the small dataset and low number of recaptures, the most consistent and precise results were obtained from a fully time-dependent version of the Jolly-Seber open-population model, with annual survival fixed at 0.96, using the MS dataset. This suggests that the WSA feeding assemblage during the months of spring and summer (September–March) of the study period numbered about 500 animals. The relationship of these whales to those (perhaps strictly migratory) that may occur in other seasons of the year, and their links to possible migratory routes and other feeding or breeding areas, remain uncertain.

Diurnal movements and behaviour of Heaviside's dolphins, Cephalorhynchus heavisidii, with some comparative data for dusky dolphins, Lagenorhynchus obscurus

The sympatric Heavisides (Cephalorhynchus heavisidii) and dusky dolphins (Lagenorhynchus obscurus) are poorly studied in South Africa and are potentially at risk from anthropogenic threats Including fisheries bycatch. As part of a larger study, shore-based observations were made in a small bay (∼1000 m wide) in the Western Cape, South Africa, during the summer months of 1999–2001 to gather data on their nearshore movements and behaviour. Heavisides dolphins exhibited a diurnal onshore—offshore migration and the sighting rate varied significantly with time of day and brightness of the moon, with numbers being markedly higher before 12:00 and nearer a full moon. These patterns were presumed to be linked to the vertical migration of their principal prey, Juvenile hake Merluccius species and Heavisides dolphins appeared to be resting and not feeding Inshore during the day. Sightings of dusky dolphin showed no predictable variation with time of day but their numbers Inshore were significantly lower when upwelllng conditions existed offshore. Larger groups of Heavisides dolphins (especially groups of four) were more active (leaps, etc.) than smaller groups, but behaviour was not linked to environmental factors. The dissimilar responses to environmental conditions suggest that sympatry in these two species is mediated by niche as well as prey differentiation.

Near-shore distribution of Heaviside’s (Cephalorhynchus heavisidii) and dusky dolphins (Lagenorhynchus obscurus) at the southern limit of their range in South Africa

Photo-identification surveys over three years along 390 km of coastline north of Cape Town, revealed that Heavisides dolphin distribution was consistent between years and higher in areas more exposed to swells and with greater long-term availability of small hake Merluccius capensis (their principal prey). Dusky dolphin sighting rates varied considerably between years, but were generally higher in areas with lower hake availability and sandier shores (mostly straighter coastline). Large groups of 50–200 dusky dolphins were only seen in St Helena Bay the site of a wind-driven upwelling zone. Heavisides dolphins were found in shallower, cooler water than dusky dolphins and were more likely to be seen during brighter phases of the moon (when nocturnal light conditions may influence the vertical migration patterns of prey) and in areas of high hake abundance, Near-shore fishing activity was higher in the northern half of the study area and clustered around harbours. Set netting occurred only at Yzerfontein and St Helena Bay, but due to changes in the industry is currently thought to be a low threat to the population. Interactions between Heavisides and dusky dolphins were usually neutral and sympatry appears to be mediated by differences in overall range and the type and size of prey species taken.

Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

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 substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information and estimated rates of gene flow using maximum‐likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographical distance (IBD P < 0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broadscale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST 0.034–0.161; P < 0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster and geneflow analyses. Instances of male fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. The relationships between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.

Fungi associated with the skin of a southern right whale (Eubalaena australis) from South Africa

Abstract Cutaneous fungi are known to affect parts of the outermost skin layers of mammals, including the epidermis, stratum spinosum and stratum corneum, as well as mucocutaneous membranes, genitalia or external ears. Relatively little is known about fungal infections of Mysticete cetaceans and studies are needed to determine the fungal diversity associated with these marine mammals. This case report was aimed at identifying the fungi associated with the skin of a diseased neonatal southern right whale (Eubalaena australis) found stranded in the Western Cape Province of South Africa. Initial physical examination on site revealed hyperplasia of the follicular and epidermal epithelium. Preliminary examination of skin biopsies using scanning electron microscopy indicated that the skin was colonized by fungal hyphae. Isolation methods yielded a number of fungal isolates, which were identified using standard morphology and rDNA sequence data. These analyses confirmed colonization of the cutaneous layers by species belonging to the genera Fusarium, Chaetomium and Penicillium. Moreover, all isolates were capable of degrading keratin, indicating that skin may act as a natural substrate for these fungi. This study is the first report of the association of these fungi with southern right whale skin.

Possible non-offspring nursing in the southern right whale, Eubalaena australis

During the austral winter, adult female southern right whales Eubalaena australis enter the South African coastal waters to give birth and raise their young. Most births take place over a 4-month period, when the females congregate in specific coastal areas or nursery grounds for up to a recorded maximum of 105 days. At this time, the density of cow—calf pairs in nursery areas can reach as high as 3.2 pairs/km2 over 26 km of coastline. Although a single young is born and suckled exclusively for 7 months to a year, recent observations on nursery grounds include 3 incidents where apparently abandoned/orphaned calves-of-the-year have been seen associating with a minimum of 2–3 different cow—calf pairs over periods of 11–38 days. Attempts to suckle from these females have been noted in 2 of the cases, with the response of the female varying from extreme avoidance to apparent tolerance. In one instance where the observations of the same trio extended over 21 days, the non-offspring appeared to compete at least equally with the offspring, even though the mother directed her evasive tactics more at the non-offspring than her own calf. At the same time, both of the calves exhibited some growth in length when compared with the size of the adult female: their subsequent survival is unknown. Non-offspring nursing in monotocous species is generally rare, and the costs to the female potentially high: this is certainly the case for seasonally feeding mysticetes such as the right whale, where the costs of lactation cannot be recovered until the cow resumes feeding about 4 months after parturition. Hence, it is perhaps not surprising that these are the first recorded observations of contemporaneous nursing attempts by offspring and non-offspring calves of any mysticete.