Pseudogenes and DNA-based diet analyses: a cautionary tale from a relatively well sampled predator-prey system

Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. However, nuclear pseudogenes that display variable similarity to the mitochondrial versions are common in many taxa. The presence of nuclear pseudogenes that co-amplify with their mitochondrial paralogues can lead to several possible confounding interpretations when applied to estimating animal diet. Here, we investigate the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose dolphins (Tursiops truncatus) that were assayed for prey DNA with a universal primer technique. We found pseudogenes in 13 of 15 samples and 1-5 pseudogene haplotypes per sample representing 5-100% of all amplicons produced. The proportion of amplicons that were pseudogenes and the diversity of prey DNA recovered per sample were highly variable and appear to be related to PCR cycling characteristics. This is a well-sampled system where we can reliably identify the putative pseudogenes and separate them from their mitochondrial paralogues using a number of recommended means. In many other cases, it would be virtually impossible to determine whether a putative prey sequence is actually a pseudogene derived from either the predator or prey DNA. The implications of this for DNA-based dietary studies, in general, are discussed.

Periodic variability in cetacean strandings: links to large-scale climate events

Cetacean strandings elicit much community and scientific interest, but few quantitative analyses have successfully identified environmental correlates to these phenomena. Data spanning 1920-2002, involving a total of 639 stranding events and 39 taxa groups from southeast Australia, were found to demonstrate a clear 11-13- year periodicity in the number of events through time. These data positively correlated with the regional persistence of both zonal (westerly) and meridional (southerly) winds, reflecting general long-term and large-scale shifts in sea-level pressure gradients. Periods of persistent zonal and meridional winds result in colder and presumably nutrient-rich waters being driven closer to southern Australia, resulting in increased biological activity in the water column during the spring months. These observations suggest that large-scale climatic events provide a powerful distal influence on the propensity for whales to strand in this region. These patterns provide a powerful quantitative framework for testing hypotheses regarding environmental links to strandings and provide managers with a potential predictive tool to prepare for years of peak stranding activity.

Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions

The DNA of prey present in animal scats may provide a valuable source of information for dietary studies. We conducted a captive feeding trial to test whether prey DNA could be reliably detected in scat samples from Steller sea lions (Eumetopias jubatus). Two sea lions were fed a diet of fish (five species) and squid (one species), and DNA was extracted from the soft component of collected scats. Most of the DNA obtained came from the predator, but prey DNA could be amplified using prey-specific primers. The four prey species fed in consistent daily proportions throughout the trial were detected in more than 90% of the scat DNA extractions. Squid and sockeye salmon, which were fed as a relatively small percentage of the daily diet, were detected as reliably as the more abundant diet items. Prey detection was erratic in scats collected when the daily diet was fed in two meals that differed in prey composition, suggesting that prey DNA is passed in meal specific pulses. Prey items that were removed from the diet following one day of feeding were only detected in scats collected within 48 h of ingestion. Proportions of fish DNA present in eight scat samples (evaluated through the screening of clone libraries) were roughly proportional to the mass of prey items consumed, raising the possibility that DNA quantification methods could provide semi-quantitative diet composition data. This study should be of broad interest to researchers studying diet since it highlights an approach that can accurately identify prey species and is not dependent on prey hard parts surviving digestion.

Metabolic limits on dive duration and swimming speed in the southern elephant seal Mirounga leonina

The ability of air-breathing marine predators to forage successfully depends on their ability to remain submerged. This is in turn related to their total O(2) stores and the rate at which these stores are used up while submerged. Body size was positively related to dive duration in a sample of 34 adult female southern elephant seals from Macquarie Island. However, there was no relationship between body size and dive depth. This indicates that smaller seals, with smaller total O(2) stores, make shorter dives than larger individuals but operate at similar depths, resulting in less time being spent at depth. Nine adult female elephant seals were also equipped with velocity time depth recorders. In eight of these seals, a plot of swimming speed against dive duration revealed a cloud of points with a clear upper boundary. This boundary could be described using regression analysis and gave a significant negative relationship in most cases. These results indicate that metabolic rate varies with activity levels, as indicated by swimming speed, and that there are quantifiable limits to the distance that a seal can travel on a dive of a given swimming speed. However, the seals rarely dive to these physiological limits, and the majority of their dives are well within their aerobic capacity. Elephant seals therefore appear to dive in a way that ensures that they have a reserve of O(2) available.

The composition of Australian fur seal (Arctocephalus pusillus doriferus) milk throughout lactation

The proximate chemical composition of milk was determined throughout lactation in the Australian fur seal (Arctocephalus pusillus doriferus Wood Jones), a temperate species with an 11-mo lactation period typical of most temperate otariids. Average lipid and protein contents were 42% and 10%, respectively, which is similar to that recorded for the polar otariid species but higher than reported in other temperate, long-lactation species. Milk composition, however, varied substantially throughout lactation, with lipid content rising from 30% soon after parturition to 50% at 230 d postpartum before decreasing to 45% toward weaning. The trend in water content was opposite to that of lipid, while protein content increased only slightly during lactation from 10% to 12%. The peak in lipid content occurred at approximately 70% of the way through lactation, similar to that found in the Australian sea lion and several phocid seal species. Significant positive relationships were found between milk lipid content and both the duration of the preceding foraging trip and body mass. A highly significant and close correlation was found between milk water and lipid contents such that gross energy content may be accurately predicted from water content alone. Similar predictive equations have been found for several other otariid and phocid species, but these appear to differ between phylogenetic groups.

Heart rate, swimming speed, and estimated oxygen consumption of a free-ranging southern elephant seal

Heart rate, swimming speed, and diving behaviour were recorded simultaneously for an adult female southern elephant seal during her postbreeding period at sea with a Wildlife Computers heart-rate time depth recorder and a velocity time depth recorder. The errors associated with data storage versus real-time data collection of these data were analysed and indicated that for events of short duration (i.e., less than 10 min or 20 sampling intervals) serious biases occur. A simple model for estimating oxygen consumption based on the estimated oxygen stores of the seal and the assumption that most, if not all, dives were aerobic produced a mean diving metabolic rate of 3.64 mL O2 kg-1, which is only 47% of the field metabolic rate estimated from allometric models. Mechanisms for reducing oxygen consumption while diving include cardiac adjustments, indicated by reductions in heart rate on all dives, and the maintenance of swimming speed at near the minimum cost of transport for most of the submerged time. Heart rate during diving was below the resting heart rate while ashore in all dives, and there was a negative relationship between the duration of a dive and the mean heart rate during that dive for dives longer than 13 min. Mean heart rates declined from 40 beats min-1 for dives of 13 min to 14 beats min-1 for dives of 37 min. Mean swimming speed per dive was 2.1 m s-1, but this also varied with dive duration. There were slight but significant increases in mean swimming speeds with increasing dive depth and duration. Both ascent and descent speeds were also higher on longer dives.

Seasonal-Variation in Water Flux, Field Metabolic-Rate and Food-Consumption of Free-Ranging Koalas (Phascolarctos-Cinereus)

Mass-corrected field metabolic rates of free-ranging male koalas in central Queensland, Australia, varied between 0.329 MJ kg0.75 day-1 in summer and 0.382 MJ kg0.75 day-1 in winter. Field water influx measured 50.8 mL kg-0.8 day-1 in winter, increasing to 59.9 mL kg0.8 day-1 in summer for the same koalas, and was positively correlated with values for leaf moisture of food. Winter rates of water influx for koalas from Springsure were lower than those recorded for koalas from Victoria for the same period of the year. Mass-corrected feeding rates were lower in summer than winter; wet food intake was significantly lower than reported for similar sized female koalas from Victoria. The preferred browse was Eucalyptus crebra in winter and E. tereticornis in summer. Our study indicates that in central Queensland seasonal changes in diet selection by male koalas reflect increased energy requirements in winter and increased water requirements in summer.

Early Growth and Milk-Composition in Southern Elephant Seals (Mirounga-Leonina)

Growth rates and changes in body composition of pups were monitored during the 3-week lactation period of southern elephant seals at Macquarie Island. Despite a slight decrease in weight in the first days post-partum, pups attained a mass of 114+/-16.6 kg (mean+/-s.d.) at weaning, representing an average growth rate of 3.53+/-0.80 kg day-1 over the entire lactation period. The proportion of body mass represented by fat was less than 3% at birth, increasing to 40.8+/-12.7% at weaning. Lean tissue mass altered little for most of the lactation period, but did show an increase in the last four days. The fat content of the milk reflected these changes, starting at 16.1+/-6.98% on Day 1 of lactation and increasing to 39.5+/-15.2% about the time of weaning. Fat content of the milk was, however, highly variable and at weaning ranged from 7% to 55%. Although the growth rate of the pup was correlated with mass lost by its mother during lactation, there was no relationship between maternal mass and weaning weight of pups. It is suggested that growth rates may be related to maternal condition and not simply mass, and, further, that differences in growth rates between populations of southern elephant seals are related to maternal energy reserves.

The Diving Behavior of Adult Male and Female Southern Elephant Seals, Mirounga-Leonina (Pinnipedia, Phocidae)

Over 50 000 individual dive records collected by time-depth recorders were analysed with respect to sex of the seal, time of year and the approximate geographic location of the dive. Six distinct dive types were described on the basis of parameters such as the amount of time spent at the maximum depth of the dive, the rate of ascent and descent, and the general form of the dive profile. These dive types were 'rest' dives, 'travel' dives, 'surface' dives, 'general non-foraging' dives, 'pelagic foraging' dives and 'benthic foraging' dives. The seals spent 90% of their time at sea submerged. Less than 2% of the time was spent on the surface in intervals of more than 10 min. A further 20-30% of the time was spent on the various non-foraging types of dives. Most females performed only 'pelagic foraging' dives, while males performed both 'pelagic' and 'benthic foraging' dives. All the 'benthic foraging' dives occurred in Area 3 (defined by water-temperature data as lying over the Antarctic Continental Shelf) and were 400-500 m deep. 'Pelagic foraging' dives occurred in all three foraging areas and ranged in depth from 200 to 1100 m. These types of dives also exhibited marked diurnal variations in depth, unlike 'benthic foraging' dives. The seals spent 10-20 min at the bottom of each 'foraging' dive, where they generally displayed a series of small changes in depth (wiggles). The size of these 'wiggles' tended to be larger in 'pelagic foraging' dives than in 'benthic foraging' dives. The diving behaviour of southern elephant seals is related to the possible prey they exploit in the Southern Ocean.

Tree Use by Individual Koalas in a Natural Forest

The home ranges and species of trees used by 20 koalas (Phascolarctos cinereus) were determined in a forest in Victoria containing 6 Eucalyptus spp. Eight animals showed a preference for a tree species from those available within their home ranges. Four koalas preferred E. viminalis, 2 E. ovata and 2 E. macrorhyncha. Preference for tree species was detected only where the preferred species was in low abundance within the animal's home range. These observations confirm that koalas may show individual differences in the species of food trees they prefer. E. viminalis, the preferred species of this population, was the predominant tree species within the home range of 15 of the koalas, which may account for the lack of evidence of preference in the majority of animals.

Habitat Use and Tree Preferences of Koalas in a Mixed Eucalypt Forest

The use of specific vegetation associations and tree species by koalas in a forest containing six Eucalyptus spp. is described. There was a positive correlation between density of koalas and the density of E. viminalis, and koalas used this species in preference to other tree species. There were seasonal differences in the use of both vegetation associations and tree species. Associations dominated by E. viminalis were preferred in most seasons. E. viminalis was the most preferred species in all seasons except summer, when E. ovata was preferred. This was not reflected in a change in preference for vegetation associations. Male koalas showed a preference for E. macrorhyncha, and to a lesser extent E. viminalis and E, ovata. Females showed a consistent preference for E. ovata and E. viminalis. Koalas showed a strong preference for large trees in all seasons, and for specific trees within species.

Tree Species Selection by Free-Ranging Koala Populations in Victoria

Tree species selection was studied in free-ranging populations of koalas [Phascolarctos cinereus] on Phillip Island and the Brisbane Ranges in Victoria. At both sites koalas were found mainly on Eucalyptus spp. but occasionally used Acacia spp. Although koalas occurred on most of the Eucalyptus spp. present, both populations showed preferences for one or two species, particularly E. viminalis. Individual koalas showed different preferences, but the majority preferred E. viminalis. Some occurred exclusively on other species even when E. viminalis was close by. Koalas also showed preference for individual trees within a species.