A conservation genetic study of threatened, endemic southern African seabirds

Doctoral Thesis


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University of Cape Town

Molecular techniques have a broad, and growing, application in the field of wildlife conservation, ranging from the systematic identification and classification of taxa, through studying genetic connectivity between populations, to parentage and individual barcoding. While they are applied to a wide range of spatial- and temporal-scales, molecular approaches complement traditional methods used to classify, investigate and understand the natural world. This study uses multiple lines of evidence, at various scales, to investigate how seabird biology influences population-level responses to changing environments. The focal area is the Agulhas-Benguela Ecosystem (ABE) along the south-western coast of Africa. Globally, biodiversity loss due to environmental change in marine ecosystems is significantly affecting the phenology, distribution, dispersal patterns, and demographic rates of organisms across trophic-levels. Broad-scale changes are occurring that have consequences for both commercial fisheries and threatened marine top-predators. Seabirds are valuable indicators of the state of marine ecosystems, and changes in their distribution and dispersal patterns may reflect those of species in lower trophic-levels. This is the case in the ABE, where some endemic seabird species are better at responding to changes in their environment than others. Twentieth century shifts in the distribution of key pelagic prey species in the ABE have had serious consequences for endemic seabirds. The African Penguin Spheniscus demersus, Cape _ Gannet Moms capensis and Cape Cormorant Phalacrocorax capensis rely on these pelagic fish, and all three species are threatened and in decline. In this study population genetic and phylogeographic methods are used to: (i) quantify levels of genetic diversity, and determine regional-scale structure within all three focal species; (ii) explore fine-scale population structure in African Penguin; and (iii) compare wild and captive populations of African Penguins. The conservation of genetic diversity is essential for the long-term persistence of species. Population genetics can help us to understand the evolutionary processes that have shaped patterns of genetic diversity in the focal species, and predict how they might respond to further environmental changes. Comparative phylogeography, combined with capture-mark- recapture models based on ringing data and annual census counts, provide the most complete picture of the micro-evolutionary forces at play in this unique ecosystem, and highlight seabird life-history characteristics may facilitate adaptation and survival under novel conditions. This is the first conservation genetic study of endemic seabirds in the ABE. Although the three focal species differ in a number of aspects of their breeding and foraging ecology, and in some life-history characteristics, they have evolved under similar selective pressures across their shared range, and represent natural replicates that allow us to determine the dominant drivers of population genetic change. Flexibility in foraging behaviour and the degree of breeding site fidelity exhibited by each of the three focal species affect the rate and effectiveness of their demographic responses to changes in their environment. Understanding connectivity among seabird populations is crucial for their long-term conservation, and has been investigated in numerous studies of seabird species from around the world. Similar to many of these, this study found very low levels of genetic structure among populations of all three focal species based on DNA sequence data, suggesting long-term gene-flow among them, despite potential physical and non-physical barriers. Overall, the patterns observed suggest that high connectivity characterises their breeding regions, and most breeding colonies, buffering the respective populations against environmental variability. These results were supported by fine-scale analyses of the African Penguin using microsatellite markers that also suggested high levels of gene-flow, which may have masked genetic signatures of the regional- and colony-level bottlenecks experienced by this species. Microsatellite-based genetic diversity and fine-scale structure were also compared among wild and captive populations of African Penguins to assess the genetic consequences of a planned conservation breeding program. The genetic composition of birds in captivity largely reflects that found in wild populations. The success of reintroduction in terms of decreasing extinction risk in the wild is uncertain, and should be implemented as part of a broader management plan that addresses the primary threats to wild populations. Further research is required to improve our understanding of many aspects of endemic southern African marine avifauna and better inform our ability to ensure their continued persistence in this system.

Includes bibliographical references.