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Current research programmes

Systematics and Conservation Genetics


Prof. Peter Ryan (PFIAO)
Asst Prof. Rauri Bowie  (University of California, Berkeley)

Research team

Dr Jacqueline Bishop (Biological Sciences, UCT)
Dawie de Swart (National Museum, Bloemfontein)
Dr Jérôme Fuchs (MNHN, Paris)
Dr Lisa Nupen (Post-doc, NZG)
Dr Rick Nuttall (National Museum, Bloemfontein)
Dr Dayo Osinubi (Post-doc, PFIAO)
Dr Bruce Robertson (U. Otago)
Dr Rob Simmons (HRA, PFIAO)
Dr Guinevere Wogan (Post-doc, UC Berkeley)
Prof. Gary Voelker (Texas A&M)


Systematics is the branch of biology most closely associated with characterizing biodiversity. It has three major scientific ‘twigs’: taxonomy, phylogenetics and biogeography. Taxonomy involves the description, naming and classifying of species and higher taxa (genera, families, orders, etc.). Phylogenetics involves placing these taxa on to the evolutionary tree of life or (in the case of phylogeography) understanding within-species evolutionary connectivity. Biogeography involves the discovery and explanation of patterns of the distribution and diversity of taxa. There is a common misconception that the systematics of birds is well understood. For example, recent phylogenetic research by Fitztitute researchers and their collaborators has shown that Darwin’s finches are not finches, but tanagers, and hawks and falcons are not closely related to one another, but evolved their predatory life styles independently. Bird systematics is a vibrant field of research thanks to recent developments in molecular genetics, combining genetic data with rigorous analysis of more traditional lines of evidence, such as morphology, behaviour and ecology. In particular, rapid advances are being made in understanding the phylogenetic relationships among bird taxa, and we are only just starting to infer the biogeographical factors that have promoted the evolutionary diversification of birds. Members of this programme tackle a range of projects to determine the origin and taxonomic status of species, to infer their phylogeographic or phylogenetic relationships, and to identify and explain patterns of species distributions and diversity.

Surprisingly, little is known about the extent of genetic structure within widely distributed African species that are not restricted to a particular habitat type. The few studies that have been conducted suggest that speciation among African vertebrates is tied to habitat and the dynamic nature of biome boundaries. In a recent paper Jérôme Fuchs and Rauri Bowie assessed the phylogeography of two sister-species of drongos, the Square-tailed Drongo Dicrurus ludwigii and Shining Drongo D. atripennis. Their results indicate that D. ludwigii consists of two strongly divergent lineages, corresponding to an eastern-southern lineage (muenznerii, ludwigii, tephrogaster) and a central-western lineage (sharpei, saturnus). The central-western lineage may be more closely related to D. atripennis, a species restricted to the Guineo-Congolian forest block, and should thus be recognised as a separate species (D. sharpei) from the eastern-southern lineage. Genetic structure is also recovered within the three primary lineages of the D. atripennis-D. ludwigii complex, suggesting that the true species diversity still remains underestimated.

African Penguin immunogenetics and health
Genetic studies of the African Penguin Spheniscus demersus have continued with former Fitz PhD student Lisa Nupen working with the Centre for Conservation Science at the National Zoological Gardens in Pretoria, SANCCOB and the Fitz to investigate variation at genes of the immune system’s major histocompatibility complex in wild and captive birds. These genes are involved in the adaptive immune response and the results will be used to inform the captive breeding programme and reintroduction of penguins. To complement this study Dr Jacqui Bishop carried out work with Honours students Vincent Naude and Gabriella Leighton to determine blood parasite prevalence data among breeding colonies of African Penguins. These studies aim to fill a number of knowledge gaps identified by the 2013 Biodiversity and Management Plan for African Penguins.

Black Sparrowhawks
PhD student Gareth Tate made good progress with the genetic component of his study on Black Sparrowhawks Accipiter melanoleucus, testing whether the recent colonisation of the Western Cape has resulted in a strong genetic founder effect. Preliminary results comparing birds from the Western Cape to individuals sampled from populations across its traditional summer rainfall breeding range indicate that Cape Town’s population is highly variable and does not represent a subset of any particular area. The findings have interesting implications for better understanding the rapid change in morph ratios observed in the species across its range in South Africa. The genetic basis colour polymorphism is being investigated in a collaborative project between Arjun Amar, Jacqui Bishop and Robert Ingle (Molecular & Cell Biology, UCT). Working with MSc student Edmund Rodseth, the project is using advanced molecular methods to better understand the genes – and their patterns of expression – involved in adult sparrowhawk colouration.

Genetic connectivity in fynbos endemic birds
Campbell Fleming recently started work on his MSc under the guidance of Jacqui Bishop, HRA  Phoebe Barnard and Peter Ryan exploring the phylogeographic history of Cape Sugarbirds Promerops cafer and Orange-breasted Sunbirds Anthobaphes violacea. The project builds on existing samples collected by Fitz post-doc Alan Lee, and will use mitochondrial and nuclear DNA markers to reconstruct recent evolutionary patterns of gene flow in these two species to help better understand the impacts that changing climate and resultant habitat availability will have on fynbos endemic birds.

Population structure of intra-African migratory birds
Fitz Post-doc Dayo Osinubi is working with Lisa Nupen and the National Zoological Gardens on a research project investigating movement ecology and genetic connectivity among populations of intra-African migratory bird species. Focal species include kingfishers, cuckoos and bee-eaters that undertake seasonal movements in Africa. Sampling commenced in Limpopo Province at the end of2015, and will continue in west Africa (Ghana, Nigeria), east Africa (Kenya, Tanzania), and southern Africa (South Africa, Zimbabwe). The aim is to use genetic and other markers (e.g. stable isotopes) to infer movement patterns among these species. The study will investigate whether currently recognized subspecies are genetically distinct, and assess levels of genetic diversity within focal species. This will allow the detection of common patterns of genetic connectivity among populations and provide information about migratory pathways across Africa. Genetic data can also be used to infer historical population expansion or contraction, identify source and sink populations, and identify hybrid zones. Target species differ in many aspects of their ecology, but likely encounter common threats during their seasonal migrations. Identifying major migratory pathways and genetic breaks will contribute to future conservation efforts and improve our understanding of intra-African migrants