Foraging ecology of the African Penguin Spheniscus demersus in relation to ocean physical processes.

Includes abstract.This research demonstrated the dual utility of bio-loggers as a method for generating accurate, high-resolution oceanographic data. These data can be used in future studies, generating a cross disciplinary platform for research. The thesis augments our knowledge base of the African Penguins foraging ecology. African Penguins show flexibility in their foraging behaviour by adjusting their dive behaviour to subsurface thermal structures. Penguins also demonstrated foraging optimization by using temperature cues and behavioral switching to maximize the probability of locating prey patches on a fine temporal and spatial scale

Understanding the decline of Martial Eagles Polemaetus bellicosus in the Kruger National Park, South Africa

Protected areas have been identified as one of the most effective strategies for reducing biodiversity loss in a world where the negative effects of global change are increasing. However for species which migrate or which range beyond the borders of protected areas, these protected areas may only offer partial protection against the threats in the surrounding landscape. Understanding the role and limitations that protected areas can play in conserving threatened species can contribute to better conservation measures for species that may otherwise not benefit from more conventional conservation approaches. The Martial Eagle is a low-density apex predator currently declining across its African range. Changes in reporting rates from bird atlas surveys suggest declines of up to 60 % over the last 20 years (1987-1982 vs. 2007-2013) across South Africa. Worryingly, large protected areas were not immune to these declines. For instance reporting rates in Kruger National Park (KNP; ca. 20,000 km²), an area often considered a stronghold for Martial Eagles, recorded a 54 % decline in reporting rates. It is not clear what the major drivers of declines have been in South Africa, nor what is contributing to the declines in these large protected areas. In this thesis I study the ecology of Martial Eagles in KNP to improve our understanding of the threats they face and how these threats at various stages in their life cycle may be driving declines within protected areas where one would expect that the species should be well conserved. I hypothesised that the main driver of declines in protected areas is that juvenile Martial Eagles disperse beyond the borders of protected areas where they are at increased risk of unnatural mortality, thus leading to recruitment failure back into even the largest protected areas. To test this hypothesis, I fitted GPS tags to 9 juvenile eagles to understand their dispersal behaviour, an aspect of their life cycle for which no previous information existed, and to explore their survival rates. During a lengthy post fledging dependency phase (7 - 9 months) birds began making exploration trips that reached up to ca. 150 km from the nest site and beyond the borders of KNP. After dispersal onset, birds ranged widely up to 390 km from their nests covering areas that averaged ca. 6,500 km²; protected areas covered only 55 % of this area. In contrast to my hypothesis survival rates did not appear particularly low; from monitoring successfully dispersed juveniles over 36 months in total, only one immature bird was confirmed to have died presumably due to natural causes. To understand adult habitat preference and ranging behaviour, which can inform habitat requirements for the species conservation, I fitted GPS tags to eight adult birds. Models of their habitat preference indicated that the species preferred to utilise areas within their home ranges that were in areas with greater tree cover, with areas of dense bush rather than open bush or grassland, amongst other important features. These results were important to identify potential threats, such as the loss of trees in Savannah's, which is currently occurring due to elephant damage and fire influences. The species held large territories (ca. 108 km²) constraining the maximum number of pairs that the Park is able to support (max. 185 possible pairs), however models of distribution suggest the available habitat in KNP likely supports ca. 60 - 70 breeding pairs. Two adult individuals never held territories and another two abandoned their territories during the course of the study. These individuals ranged widely (ca. 44,000 km²) suggesting a floater population exists in the region. The death of three of these four floater individuals (two persecutions and an electrocution) indicates that adults are particularly at risk of mortality during these wide-ranging movements beyond protected area boundaries. Two natural mortalities of territorial birds within the park were also recorded. Overall therefore, despite our relatively small sample size, adult birds do appear to have worryingly low survival rates. Because my sample size of both adults and juveniles/immatures was relatively small (adults = 8, juveniles = 9), their movements may not be fully representative of the entire population. Therefore, I additionally modelled the distribution of Martial Eagles using independent sightings data to describe suitable areas for the species both within the KNP and adjacent areas (within ca. 400 km of the park). Identifying these areas provides conservation managers with more information to ensure adequate conservation measures are in place for this species in these areas. At least 29 % of KNP was predicted to be suitable for Martial Eagles, while neighbouring regions in Mozambique and Swaziland were also predicted to be highly suitable for the species. Given the adult mortalities and general scarcity of Martial Eagles in Mozambique the area may act as a population sink for KNP birds. Lastly, I compared current reproductive parameters to those reported in a considerable number of other studies on the species both within KNP and elsewhere. Productivity recorded during this study was lower than any previously recorded estimate. Using a population model, I show that current productivity within KNP is sufficiently low to have been solely responsible for the known levels of decline there, without the need to invoke any other contributory factors. A high hatching failure rate was mostly responsible for the low productivity. However, it is important to note that at least two of the three years of data collection occurred during low (drought) rainfall years, which may have constrained breeding, and thus may not be reflective of productivity levels more generally over the recent longer term. My research helps identify the most likely drivers of population declines in KNP, suggesting that elevated adult mortality and lower productivity may be the key factors. Drivers of low productivity require further investigation, however it is likely that changes in habitat quality or climate may be impacting on the species within KNP. The study also highlighted the difficulty of conserving wideranging and threatened species in protected areas, which may be prone to high mortality in the surrounding landscape. This research is therefore applicable to a number of species that range widely from KNP e.g. vultures, or migratory eagles. The research indicates that protected areas alone are unlikely to conserve these species and that additional conservation measures, such as education programmes, or trans boundary policy should be put in place to realise successful conservation for these species

Phenotypic convergence in genetically distinct lineages of a Rhinolophus species complex (Mammalia, Chiroptera)

Phenotypes of distantly related species may converge through adaptation to similar habitats and/or because they share biological constraints that limit the phenotypic variants produced. A common theme in bats is the sympatric occurrence of cryptic species that are convergent in morphology but divergent in echolocation frequency, suggesting that echolocation may facilitate niche partitioning, reducing competition. If so, allopatric populations freed from competition, could converge in both morphology and echolocation provided they occupy similar niches or share biological constraints. We investigated the evolutionary history of a widely distributed African horseshoe bat, Rhinolophus darlingi , in the context of phenotypic convergence. We used phylogenetic inference to identify and date lineage divergence together with phenotypic comparisons and ecological niche modelling to identify morphological and geographical correlates of those lineages. Our results indicate that R. darlingi is paraphyletic, the eastern and western parts of its distribution forming two distinct non-sister lineages that diverged ~9.7 Mya. We retain R. darlingi for the eastern lineage and argue that the western lineage, currently the sub-species R . d. damarensis , should be elevated to full species status. R. damarensis comprises two lineages that diverged ~5 Mya. Our findings concur with patterns of divergence of other co-distributed taxa which are associated with increased regional aridification between 7-5 Mya suggesting possible vicariant evolution. The morphology and echolocation calls of R. darlingi and R. damarensis are convergent despite occupying different biomes. This suggests that adaptation to similar habitats is not responsible for the convergence. Furthermore, R. darlingi forms part of a clade comprising species that are bigger and echolocate at lower frequencies than R. darlingi , suggesting that biological constraints are unlikely to have influenced the convergence. Instead, the striking similarity in morphology and sensory biology are probably the result of neutral evolutionary processes, resulting in the independent evolution of similar phenotypes

Ranging behaviour and habitat preferences of the Martial Eagle: Implications for the conservation of a declining apex predator

<div><p>Understanding the ranging behaviours of species can be helpful in effective conservation planning. However, for many species that are rare, occur at low densities, or occupy challenging environments, this information is often lacking. The Martial Eagle (<i>Polemaetus bellicosus</i>) is a low density apex predator declining in both non-protected and protected areas in southern Africa, and little is known about its ranging behaviour. We use GPS tags fitted to Martial Eagles (n = 8) in Kruger National Park (KNP), South Africa to describe their ranging behaviour and habitat preference. This represents the first time that such movements have been quantified in adult Martial Eagles. Territorial eagles (n = 6) held home ranges averaging ca. 108 km². Home range estimates were similar to expectations based on inter-nest distances, and these large home range sizes could constrain the carrying capacity of even the largest conservation areas. Two tagged individuals classed as adults on plumage apparently did not hold a territory, and accordingly ranged more widely (ca. 44,000 km²), and beyond KNP boundaries as floaters. Another two territorial individuals abandoned their territories and joined the ‘floater’ population, and so ranged widely after leaving their territories. These unexpected movements after territory abandonment could indicate underlying environmental degradation. Relatively high mortality of these wide-ranging ‘floaters’ due to anthropogenic causes (three of four) raises further concerns for the species’ persistence. Habitat preference models suggested Martial Eagles used areas preferentially that were closer to rivers, had higher tree cover, and were classed as dense bush rather than open bush or grassland. These results can be used by conservation managers to help guide actions to preserve breeding Martial Eagles at an appropriate spatial scale.</p></div

Tracking data summary for adult Martial Eagles GPS tracked in KNP.

<p>The attributed causes of transmission cessation are shown where applicable; devices still transmitting at the time of publication are represented by NA.</p

Movements of floater adult Martial Eagles (G32551 and G32516), and those that were territorial but vacated their territories (PTT 72154 and G32553) from KNP, showing the area covered during tracking.

<p>GPS locations are coloured by month to visualize movements through time (see bottom legend). The location of each bird’s death, or last known location, is also indicated.</p

Generalized linear mixed model (GLMM) predictive fixed-effects plots showing the modelled habitat utilization of territorial Martial Eagles tracked after their capture in KNP according to several habitat features: tree cover, elevation, topographic slope, distance to nearest river, distance to nearest road, and land cover.

<p>Solid lines show the predicted relationships, with 95% CL captured within grey shaded areas. The bottom right panel shows the predicted probability for the categorical factor, land cover, with 95% confidence limits represented by vertical lines.</p

The 95% kernel density estimate (KDE) home range sizes for each individual by month.

<p>Missing bars indicate no data due to cessation of tag transmission. Coloured bars indicate months in which the individual bird was recorded to incubate (red), raise a fledgling (blue) or provision a fledged chick in post fledging dependency (green). Horizontal dashed lines indicate the 95% KDE for the entire dataset of each individual. Vertical lines indicate the proportion of days per month that a nest site was visited by the individual. * 1493 km²; ** 2319 km²</p

Frequency of step lengths in 1 km (0–10 km) and 15 km (10–100 km) intervals (left), and fixed effects plots from a generalised linear mixed model investigating step lengths between the breeding and non-breeding period (centre) and between months to assess seasonality (right).

<p>Frequency of step lengths in 1 km (0–10 km) and 15 km (10–100 km) intervals (left), and fixed effects plots from a generalised linear mixed model investigating step lengths between the breeding and non-breeding period (centre) and between months to assess seasonality (right).</p

Home range estimators (50, 75, 95% Kernel Density Estimates) for six of eight adult Martial Eagles that were classed as territorial.

<p>Eagles were GPS tracked in KNP, South Africa (top left). Home ranges are shown in relation to KNP borders. Expanded plots of home ranges are shown (right) in relation to the KNP boundary (thick black line), main rivers (blue lines e.g. Timbavati), roads (thin parallel black lines e.g. S39, nest sites (green trees), and capture locations (red stars). Panels on the right showing home ranges are set to the same scale as given in the upper right panel.</p