Reduced availability of high energy-content prey (nutritional stress) is a predominant hypothesis to explain the decline of Steller sea lion (Eumetopias jubatus) populations in western Alaska from the late 1970'€™s to the late 1990'™s. Animals may physiologically respond to consuming insufficient prey by increasing stress levels and decreasing metabolic rates. It may thus be possible to identify nutritional stress by measuring concentrations of glucocorticoids (stress) and thyroid hormones (metabolism) shed in feces. However, techniques to measure thyroid hormone concentrations from Steller sea lion feces have not been developed. We quantified variation of triiodothyronine (T3) and thyroxine (T4) concentrations in Steller sea lion feces following injections of thyrotropin (TSH) into four captive animals. Glucocorticoids (GC) were also assayed to examine any relationship to stimulated thyroid hormone secretion. We found that fecal T3 peaked 48 h post-injection and increased 25-57% in three sea lions (all animals, p=0.03). Pre-injection GC increases indicated stress from isolation for baseline fecal collections, but post-injection increases could not be confirmed as a response to TSH injections or as a product of the study design. The results demonstrated that pre- and post-injection changes in fecal GC and T3 concentrations were consistent with predictions of an increased stress response and metabolic rate within the animals. We then measured T3 and GC concentrations in 834 Steller sea lion fecal samples collected in 2005 and 2006 from 15 sites (haulouts and rookeries) between British Columbia and the Central Aleutian Islands. Overall, GC concentrations did not differ between haulout populations (western 2006 pre-pupping and eastern 2005 post-pupping). Fecal hard-part analyses revealed a lower energy-content diet in the western population, suggesting that diet quality is a relevant hypothesis to explain slightly higher GC concentrations found in the western population, specifically the Aleutian Islands region. However, nutritional stress could not be substantiated through T3 concentrations. The rookeries possessed the highest energy-content diets, but also exhibited a nutritional stress response with a significantly higher GC and lower T3 concentration than either haulout population (possibly related to lactation or decreased foraging opportunities), but T3 comparisons performed at scales of site and region were inconclusive.

Sequence variation was examined for the Zinc-finger Y (zfy) gene and the mitochondrial control region for two species of pinnipeds, the Steller sea lion (Eumetopias jubatus) and harbor seal (Phoca vitulina). The two species differ in aspects of their breeding strategies, dispersal, and life histories. Comparable stock sample sizes of males from each species were taken from localities that span at least one wellrecognized phylogeographic stock as defined by mtDNA markers. Variation in zfy, a strictly paternally inherited marker located on the Y chromosome, was low in both species. An interesting pattern of subdivision was found for zfy in harbor seals that was concordant with population subdivision for mtDNA. In Steller sea lions, no such concordant pattern was evident with only a single rare zfy variant being observed. One explanation for the different patterns observed is that dispersal is less in male harbor seals than in male Steller sea lions.

The vibrissal system of pinnipeds relies on sturdy, specialized vibrissae and supporting neural architecture apparently designed for the reception of waterborne disturbances. Although it is known that pinnipeds can use their vibrissae for fine-scale tactile discrimination and hydrodynamic detection, many aspects of vibrissal function remain poorly understood. The present work examined the adaptive significance of vibrissal structure, the sensitivity of the vibrissal system, and the signals received by this system. All of these points were considered with respect to their function in hydrodynamic reception. Four methods of study: laser vibrometry, computed tomography (CT) scanning, psychophysical testing and animal-borne tagging were used to investigate the functioning of this sensory system. Laser vibrometer recordings were used to investigate the effect of vibrissal surface structure and orientation on flow-induced vibrations in excised vibrissae. Vibrations were recorded from the shaft of excised vibrissae exposed to laminar water flow in a flume tank. Samples from three pinniped species were tested: the harbor seal (Phoca vitulina), northern elephant seal (Mirounga angustirostris) and California sea lion (Zalophus californianus). The vibrissae of the seals had an undulated surface structure, while the vibrissae of the sea lion had a smooth surface. No significant difference between species, and therefore surface structure, was observed. However, when vibrissae were tested at three angles of orientation to the water flow, a strong effect of orientation on vibration frequency and velocity was observed across species. CT scanning data revealed that the vibrissae of all the species tested had flattened cross-sectional profiles. This cross-sectional flattening could account for the observed orientation effects. Furthermore, this morphological characteristic may represent an adaptation for improved functioning in the aquatic environment by reducing self-induced-noise from swimming and potentially enhancing detection of signals from other planes. Psychophysical testing was conducted with a trained harbor seal in order to investigate the sensitivity of the vibrissal system of this species. A behavioral procedure was used to measure absolute detection thresholds for sinusoidal stimuli delivered to the vibrissae by a vibrating plate. Thresholds were measured at 9 discrete frequencies from 10 to 1000 Hz. The seal's performance in this stimulus detection task showed that the vibrissal array was sensitive to directly coupled vibrations across the range of frequencies tested, with best sensitivity of 0.09 mm/s at 80 Hz. The velocity thresholds as a function of frequency showed a characteristic U-shaped curve with a gradual low-frequency roll-off below 80 Hz and a steeper high-frequency roll-off above 250 Hz. The thresholds measured for the harbor seal in this study were about 100 times more sensitive than previous in-air measures of vibrissal sensitivity for this species. The results were similar to those reported by others for the detection of waterborne vibrations, but show an extended range of frequency sensitivity. Animal-borne tagging methods were used to investigate the signals received by the vibrissae and better understand the relevant signal components involved in hydrodynamic detection. A novel tagging system, wLogger, was developed to record vibrations directly from a vibrissa by means of an accelerometer coupled to the vibrissal shaft. Laboratory testing using excised whiskers in a water flume confirmed that the tag is capable of recording vibrational signals without hampering the natural movement of the vibrissa. In addition, the tag successfully measured vibrations from the vibrissae of a harbor seal during active swimming and hydrodynamic detection. Live animal testing, along with the supplemental recordings from excised vibrissae, revealed that interaction with hydrodynamic disturbances disrupted the vibrational signal received by the whisker. When exposed to a hydrodynamic signal, whisker vibrations increased in bandwidth, spreading energy across a wider range of frequencies. This finding suggests that modulation of the vibrational signal may play a key role in the detection of hydrodynamic stimuli by the seal. The results of this dissertation research provide insight into the functioning of the vibrissal system in pinnipeds and establishes the groundwork for future pathways of investigation. By investigating the vibrissal system from the focal points of structure, sensitivity and received signals, a more comprehensive understanding of this refined sensory modality is emerging.

Reduced availability of high energy-content prey (nutritional stress) is a predominant hypothesis to explain the decline of Steller sea lion (Eumetopias jubatus) populations in western Alaska from the late 1970'€™s to the late 1990'™s. Animals may physiologically respond to consuming insufficient prey by increasing stress levels and decreasing metabolic rates. It may thus be possible to identify nutritional stress by measuring concentrations of glucocorticoids (stress) and thyroid hormones (metabolism) shed in feces. However, techniques to measure thyroid hormone concentrations from Steller sea lion feces have not been developed. We quantified variation of triiodothyronine (T3) and thyroxine (T4) concentrations in Steller sea lion feces following injections of thyrotropin (TSH) into four captive animals. Glucocorticoids (GC) were also assayed to examine any relationship to stimulated thyroid hormone secretion. We found that fecal T3 peaked 48 h post-injection and increased 25-57% in three sea lions (all animals, p=0.03). Pre-injection GC increases indicated stress from isolation for baseline fecal collections, but post-injection increases could not be confirmed as a response to TSH injections or as a product of the study design. The results demonstrated that pre- and post-injection changes in fecal GC and T3 concentrations were consistent with predictions of an increased stress response and metabolic rate within the animals. We then measured T3 and GC concentrations in 834 Steller sea lion fecal samples collected in 2005 and 2006 from 15 sites (haulouts and rookeries) between British Columbia and the Central Aleutian Islands. Overall, GC concentrations did not differ between haulout populations (western 2006 pre-pupping and eastern 2005 post-pupping). Fecal hard-part analyses revealed a lower energy-content diet in the western population, suggesting that diet quality is a relevant hypothesis to explain slightly higher GC concentrations found in the western population, specifically the Aleutian Islands region. However, nutritional stress could not be substantiated through T3 concentrations. The rookeries possessed the highest energy-content diets, but also exhibited a nutritional stress response with a significantly higher GC and lower T3 concentration than either haulout population (possibly related to lactation or decreased foraging opportunities), but T3 comparisons performed at scales of site and region were inconclusive.

Reduced availability of high energy-content prey (nutritional stress) is a predominant hypothesis to explain the decline of Steller sea lion (Eumetopias jubatus) populations in western Alaska from the late 1970' s to the late 1990' s. Animals may physiologically respond to consuming insufficient prey by increasing stress levels and decreasing metabolic rates. It may thus be possible to identify nutritional stress by measuring concentrations of glucocorticoids (stress) and thyroid hormones (metabolism) shed in feces. However, techniques to measure thyroid hormone concentrations from Steller sea lion feces have not been developed. We quantified variation of triiodothyronine (T3) and thyroxine (T4) concentrations in Steller sea lion feces following injections of thyrotropin (TSH) into four captive animals. Glucocorticoids (GC) were also assayed to examine any relationship to stimulated thyroid hormone secretion. We found that fecal T3 peaked 48 h post-injection and increased 25-57% in three sea lions (all animals, p=0.03). Pre-injection GC increases indicated stress from isolation for baseline fecal collections, but post-injection increases could not be confirmed as a response to TSH injections or as a product of the study design. The results demonstrated that pre- and post-injection changes in fecal GC and T3 concentrations were consistent with predictions of an increased stress response and metabolic rate within the animals. We then measured T3 and GC concentrations in 834 Steller sea lion fecal samples collected in 2005 and 2006 from 15 sites (haulouts and rookeries) between British Columbia and the Central Aleutian Islands. Overall, GC concentrations did not differ between haulout populations (western 2006 pre-pupping and eastern 2005 post-pupping). Fecal hard-part analyses revealed a lower energy-content diet in the western population, suggesting that diet quality is a relevant hypothesis to explain slightly higher GC concentrations found in the western population, specifically the Aleutian Islands region. However, nutritional stress could not be substantiated through T3 concentrations. The rookeries possessed the highest energy-content diets, but also exhibited a nutritional stress response with a significantly higher GC and lower T3 concentration than either haulout population (possibly related to lactation or decreased foraging opportunities), but T3 comparisons performed at scales of site and region were inconclusive. / Science, Faculty of / Zoology, Department of / Graduate

Weddell seals (Leptonychotes weddellii) are among the deepest diving pinnipeds (i.e., seals, sea lions, and walrus) and one of the best studied marine mammals in the world; as such, these seals are considered a model species for the study of diving physiology and behavior. Adult Weddell seal dive physiology is rather comprehensively understood, yet previous research has excluded an examination of pups’ initial independent diving attempts, beginning instead with the diving capabilities of near-weaning individuals at four to five weeks of age. This is beyond the point many pups have attempted their first independent dives; pups begin to enter the water at 8-10 days after birth, with some observed in the water earlier. The aim of this study was to investigate the development of diving capabilities and fine-scale behaviors of Weddell seal pups beginning at one week of age throughout their dependence period. Pups were sampled longitudinally at 1, 3, 5, and 7 weeks of age. Total body oxygen stores (TBO2, mL O2) were calculated as the sum of blood, muscle, and lung oxygen stores for each seal at all time points. Blood samples were collected under sedation, muscle oxygen parameters were interpolated, and lung oxygen content was extrapolated from adult values. Flipper-mounted time-depth recorders were used to collect concurrent dive behavior data. In chapter 1, I hypothesized that diving capability (TBO2) would be more strongly correlated with dive experience than calendar age; to examine this, age, mass, and diving parameters were correlated with oxygen stores. I instead found mass and age were most significantly correlated with individual tissue oxygen stores and TBO2. I predicted diving experience would be an important driver of oxygen storage development due to hypoxia exposure, but pups spent the majority of their time in the water at the surface and had little to no exposure to hypoxia during dependence. Increases in mass may enable early advances in diving ability, and with increased diving capabilities, pups will be able to become successful independent foragers. Later exposure to hypoxia may be the key to the subsequent increases in TBO2 observed in yearlings and juveniles. In chapter 2, I used TDR data to predict when pups would be in the water based on developmental, temporal, and environmental factors including age, weaning status, time of day, and weather parameters. Pups spent the most time in the water and made their deepest, longest, and most frequent dives during the late night and early morning hours. These data indicate pups are following the diving patterns of their mothers, which follow the diurnal vertical migration of their prey. The data also suggest Weddell seal pups most likely prioritize learning to swim and navigate as opposed to practicing foraging while still dependent. It is critical for pups to develop their swimming, navigational, and diving abilities while they are still with their moms to ensure their survival. This study is the first to describe the complete trajectory of the development of diving physiology and behavior in Weddell seal pups throughout dependence. It is important to understand how the internal diving physiology of Weddell seal pups develops because this directly determines their diving capabilities and their ability to forage successfully, which in turn directly correlates with their survival. Pup survival is an indicator of population growth rates, so the development of diving physiology in pups can lend insights into larger population-level trends.

Polygyny is the most common mating system in mammalian species (95%), yet our understanding of polygynous systems and microevolutionary processes is still limited. Pinniped mating systems range from extreme polygyny (e.g. elephant seals) to sequential female defence by males and hence have often been used as models for mating system studies. Parentage analysis has enabled the examination of mating success, the identification of pedigrees, and the elucidation of social organisation, greatly enhancing our understanding of mating systems (Chapter 1). However, such analyses are not without pitfalls, with erroneous assignments common in open systems (i.e. when parental and offspring samplings are incomplete). We investigated the effects of the user-defined parameters on the accuracy of parental assignment using two commonly used parental allocation programme, CERVUS and PASOS (Chapter 2). We showed that inaccurate user-defined parameters in CERVUS and PASOS can lead to highly biased output e.g. the assignment rate at 95% CL of offspring with a sampled known mother to sampled males decreased from 58% to 32% when the proportion of candidate males sampled in the parameter options decreasing 4-fold. We found that the use of both CERVUS and PASOS for parentage assignment can increase the likelihood of correctly allocating offspring to sampled parents to 97% in our study system. Incorrect parental assignment can bias estimates of various biological parameters, such as lifetime reproductive success and mate choice preference, and hence bias ecological and evolutionary interpretations. Here, we propose solutions to increase the power of parentage assignment and hence decrease the bias in biological parameter estimates. In addition, we analysed the effects of the intrinsic bias in likelihood assignment approaches towards assigning higher probability of parentage on individuals with rare alleles and those with heightened offspring-parent matches, which increase with the number of homozygous loci (Chapter 3). We showed that, as a consequence of the algorithms employed in the programmes CERVUS and PASOS, heterozygote males with rare genotypes are assigned higher rates of parentage than males with common alleles. Consequently, where two males could both be biological fathers of a given offspring, parentage assignment will more often go to the male with the rarer alleles (most often in heterozygous loci). Thus, the commonly used parentage assignment methods may systematically bias the results of parentage analyses towards supporting the notion that females prefer more genetically unusual, most often heterozygous, males. Such a bias may sway investigators towards incorrectly supporting the concept that females choose genetically more unusual males for heterozygosity fitness benefits that underpin the good genes hypothesis, when in fact no such relationship may exist. In polygynous mammals, successful males mate with multiple females by competing with and limiting the access of other males to females. When the status of many males (age, size, health, genetic etc.) prevents them from achieving the primary mating tactic, theory predicts selection for a diversification of male mating tactics. Recent studies in pinnipeds have shown that observed male mating success was correlated to male paternity success in some species (elephant-seals), but not in others (grey seals). The existence of alternative mating strategies can explain those discrepancies. Chapter 4 implemented the guidelines provided in Chapter 2 and 3 and focused on the polygynous New Zealand fur seal Arctocephalus forsteri, predicting that 1) competition for females is likely to cause a diversification of male mating tactics; and 2) that alternative tactics can yield reproductive success. Our results indicated three male behavioural profiles; one corresponded to large territorial males and two illustrated a continuum of alternative tactics employed by non-territorial subordinate males. Our study highlights that holding a territory is not a necessary condition for reproductive success in a population of otariids. The degree of sexual size dimorphism in polygynous species is expected to increase with the degree of intra-sexual competition and in turn with the degree of polygyny. The life history of an individual is the pattern of resource allocations to growth, maintenance, and reproduction throughout its lifetime. Both females and males incur viability costs of mating and reproduction. However, male viability costs due to increase growth and male-male competition can be greater than female viability costs of mate choice and reproduction. Although an abundant literature on sexual dimorphism in morphology, physiology, and parasite infections is available, little is known on the intra-sexual differences in physiology and parasite infections associated to the reproductive success of different mating strategies in mammalian species. Chapter 5 examined the reproductive costs between territorial and subordinate males New Zealand fur seal related to their relative reproductive success using a multidisciplinary approach (behaviour, genetics, endocrinology, parasitology). We found that dominant New Zealand fur seal males endure higher reproductive costs due to the direct and indirect effects of high testosterone levels and parasite burdens. Our study highlights that holding a territory confers a higher reproductive success, but induces higher costs of reproduction that may impair survival. Understanding microevolutionary processes associated to polygynous systems is fundamental in light of the ongoing anthropogenic alteration of the environment through climatic variations and habitat reduction which ultimately affect opportunity for sexual selection and shape the life history trade-offs.

For young animals, surviving the first year of nutritional independence requires rapid development of effective foraging behaviour before the onset of terminal starvation. Grey seal (Halichoerus grypus) pups are abandoned on the natal colony after a brief (15-21 days) suckling period and must learn to dive and forage without parental instruction. Regional and sex-specific differences in diet and foraging behaviour have been described for adults and juveniles, but the early-life behaviour of pups during the critical first months at sea remains poorly understood. This thesis investigates sources of intrinsic and extrinsic variation in the development of foraging behaviour and resource selection in grey seal pups. The studies presented here feature tracking and dive data collected from 52 recently-weaned pups, tagged at six different breeding colonies in two geographically-distinct regions of the United Kingdom (UK). Original aspects of this thesis include: (Chapter I) a comprehensive review of analytical methods for inferring foraging behaviour from tracking and dive data in pinnipeds; (Chapter II) description and comparison of regional and sex differences in movements and diving characteristics of recently-weaned pups during their first trips at sea; (Chapter III) implementation of a novel generalized hidden Markov modelling (HMM) technique to investigate the development of foraging movement patterns whilst accounting for sources of intrinsic (age, sex) and extrinsic (regional) variation; and (Chapter IV) the first analysis of grey seal pup foraging habitat preference, incorporating behavioural inferences from HMMs and investigating changes in preference through time.

The sense of smell in marine mammals is traditionally thought to be poor. However, increasing evidence suggests that pinnipeds may use their sense of smell in a variety of behavioral contexts including communication, foraging, food selection, and reproduction. Using a food-rewarded two-choice instrumental conditioning paradigm, I assessed the ability of South African fur seals, Arctocephalus pusillus, to discriminate between 12 enantiomeric odor pairs, that is, between odorants that are identical in structure except for chirality. The fur seals significantly discriminated between eight out of the twelve odor pairs (according to p < 0.05, with carvone, dihydrocarvone, dihydrocarveol, limonene oxide, menthol, beta-citronellol, fenchone, and alpha-pinene), and failed with only four odor pairs (isopulegol, rose oxide, limonene, and camphor). No significant differences in performance were found between the animals (p > 0.05). Cross-species comparisons between the olfactory performance of the fur seals and that of other species previously tested on the same set of odor pairs lend further support to the notion that the relative size of the olfactory bulbs is not a reliable predictor of olfactory discrimination abilities. The results of the present study suggest that sense of smell may play an important and hitherto underestimated role in regulating the behavior of fur seals.

Polygyny is the most common mating system in mammalian species (95%), yet our understanding of polygynous systems and microevolutionary processes is still limited. Pinniped mating systems range from extreme polygyny (e.g. elephant seals) to sequential female defence by males and hence have often been used as models for mating system studies. Parentage analysis has enabled the examination of mating success, the identification of pedigrees, and the elucidation of social organisation, greatly enhancing our understanding of mating systems (Chapter 1). However, such analyses are not without pitfalls, with erroneous assignments common in open systems (i.e. when parental and offspring samplings are incomplete). We investigated the effects of the user-defined parameters on the accuracy of parental assignment using two commonly used parental allocation programme, CERVUS and PASOS (Chapter 2). We showed that inaccurate user-defined parameters in CERVUS and PASOS can lead to highly biased output e.g. the assignment rate at 95% CL of offspring with a sampled known mother to sampled males decreased from 58% to 32% when the proportion of candidate males sampled in the parameter options decreasing 4-fold. We found that the use of both CERVUS and PASOS for parentage assignment can increase the likelihood of correctly allocating offspring to sampled parents to 97% in our study system. Incorrect parental assignment can bias estimates of various biological parameters, such as lifetime reproductive success and mate choice preference, and hence bias ecological and evolutionary interpretations. Here, we propose solutions to increase the power of parentage assignment and hence decrease the bias in biological parameter estimates. In addition, we analysed the effects of the intrinsic bias in likelihood assignment approaches towards assigning higher probability of parentage on individuals with rare alleles and those with heightened offspring-parent matches, which increase with the number of homozygous loci (Chapter 3). We showed that, as a consequence of the algorithms employed in the programmes CERVUS and PASOS, heterozygote males with rare genotypes are assigned higher rates of parentage than males with common alleles. Consequently, where two males could both be biological fathers of a given offspring, parentage assignment will more often go to the male with the rarer alleles (most often in heterozygous loci). Thus, the commonly used parentage assignment methods may systematically bias the results of parentage analyses towards supporting the notion that females prefer more genetically unusual, most often heterozygous, males. Such a bias may sway investigators towards incorrectly supporting the concept that females choose genetically more unusual males for heterozygosity fitness benefits that underpin the good genes hypothesis, when in fact no such relationship may exist. In polygynous mammals, successful males mate with multiple females by competing with and limiting the access of other males to females. When the status of many males (age, size, health, genetic etc.) prevents them from achieving the primary mating tactic, theory predicts selection for a diversification of male mating tactics. Recent studies in pinnipeds have shown that observed male mating success was correlated to male paternity success in some species (elephant-seals), but not in others (grey seals). The existence of alternative mating strategies can explain those discrepancies. Chapter 4 implemented the guidelines provided in Chapter 2 and 3 and focused on the polygynous New Zealand fur seal Arctocephalus forsteri, predicting that 1) competition for females is likely to cause a diversification of male mating tactics; and 2) that alternative tactics can yield reproductive success. Our results indicated three male behavioural profiles; one corresponded to large territorial males and two illustrated a continuum of alternative tactics employed by non-territorial subordinate males. Our study highlights that holding a territory is not a necessary condition for reproductive success in a population of otariids. The degree of sexual size dimorphism in polygynous species is expected to increase with the degree of intra-sexual competition and in turn with the degree of polygyny. The life history of an individual is the pattern of resource allocations to growth, maintenance, and reproduction throughout its lifetime. Both females and males incur viability costs of mating and reproduction. However, male viability costs due to increase growth and male-male competition can be greater than female viability costs of mate choice and reproduction. Although an abundant literature on sexual dimorphism in morphology, physiology, and parasite infections is available, little is known on the intra-sexual differences in physiology and parasite infections associated to the reproductive success of different mating strategies in mammalian species. Chapter 5 examined the reproductive costs between territorial and subordinate males New Zealand fur seal related to their relative reproductive success using a multidisciplinary approach (behaviour, genetics, endocrinology, parasitology). We found that dominant New Zealand fur seal males endure higher reproductive costs due to the direct and indirect effects of high testosterone levels and parasite burdens. Our study highlights that holding a territory confers a higher reproductive success, but induces higher costs of reproduction that may impair survival. Understanding microevolutionary processes associated to polygynous systems is fundamental in light of the ongoing anthropogenic alteration of the environment through climatic variations and habitat reduction which ultimately affect opportunity for sexual selection and shape the life history trade-offs.