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Current Research Programmes

Systematics & Biogeography

Coordinators

Prof. Tim Crowe (PFIAO)
Prof. Paulette Bloomer (University of Pretoria)
Prof. Peter Ryan (PFIAO)
Asst Prof. Rauri Bowie  (University of California, Berkeley)

Research team

Dr John Bates (Field Museum of Natural History, Chicago)
Dr Tim Bray (Postdoctoral Fellow, University of Pretoria)
Prof. Michael Bruford (Cardiff University)
Prof. Terry Burke (University of Sheffield)
Prof. Adrian Craig (Rhodes University)
Dr Michael Double (Australian National University)
Dr Christine Dranzoa (Makerere University, Uganda)
Dr Gareth Dyke (University College, Dublin)
Dr J. Steven Farris (Swedish Museum of Natural History, Stockholm)
Prof. Jon Fjeldså (Zoological Museum, University of Copenhagen)
Dr Jérôme Fuchs (Postdoctoral Fellow, PFIAO)
Dr Pablo Goloboff (Instituto Superior de Entomología, Argentina)
Dr Shannon Hackett (Field Museum of Natural History, Chicago)
Prof. Bengt Hansson (Lund University, Sweden)
Prof. Martine Hausberger (University of Rennes, France)
Prof. Terry Hedderson (Department of Botany, UCT)
Charles Kahindo (Makerere University of Kampala, Uganda)
Cecilia Kopuchian (Tucuman University)
Prof. Graham Louw (UCT Medical School)
Tshifhiwa Mandiwana-Neudani (Department of Botany, UCT)
Dr Martim Melo (Postdoctoral Fellow, PFIAO, and CIBIO, Portugal)
Michael Mills (Birding Africa; former PFIAO student)
Rick Nuttall (National Museum, Bloemfontein)
Dr Colleen O'Ryan (Department of Molecular and Cell Biology, UCT)
Asst Prof. Bret Payseur (University of Wisconsin)
Dr Eric Sande (Makerere University, Uganda)
Prof. Jon Slate (University of Sheffield)
Dr Hanneline Smit (Postdoctoral Fellow, University of Stellenbosch)
Prof. Mike Sorenson (Boston University)
Martin Stervander (MSc student, University of Lund)
Alex van Rensburg (MSc student, University of Pretoria)
Dr Bettine van Vuuren (University of Stellenbosch)
Dr Gary Voelker (Texas A. & M. University of Memphis)

Overview

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.

The comparative radiation of larks in northeast and southwest Africa

Research Team: Keith Barnes, Per Alstrom, Keith Barker, Peter Ryan & Paulette Bloomer

Larks are an ancient and highly distinct bird family, occurring predominantly in Africa. They are characterised by high levels of endemism, often at very local scales, and major radiations have taken place in the northeast and southwest arid zones of Africa. Keith Barnes studied the relationships among African larks for his PhD (completed 2007). Papers arising from this work are being finalized for publication.

Taxonomy, phylogeny and biogeography of African cisticolas

Research team: Owen Davies & Tim Crowe

This study will focus on the systematics and taxonomy of the cisticolas and, particularly, the historical treatment of the genus with respect to the seminal work done by Rear Admiral Lynes in the 1930’s who suggested natural groupings of species. It will include a focussed and detailed investigation into the systematics, taxonomy and biogeography of ‘marsh cisticolas’ using a multifaceted approach and all available evidence (including morphology, vocalisations and molecular data). Due to their strong wetland affinities, the evolutionary history of this group of birds will also provide insights into palaeo-vegetative dynamics and drainage basin evolution on the continent.

Evolution and hybridisation in Nesospiza buntings at Tristan da Cunha

Research team: Peter Ryan & Martin Stervander

Nesospiza buntings present a fascinating case study of evolution in action. Two species co-occur at Nightingale Island (4 km2), differing mainly in size. The rare, large-billed Wilkins’ Bunting N. wilkinsi feeds largely on the woody fruits of Island Trees Phylica arborea, whereas the small-billed Nightingale Bunting N. questi is an abundant dietary generalist. Small and large-billed buntings also occur on larger Inaccessible Island (14 km2), but segregation among taxa here is incomplete. Given widespread hybridisation among taxa at the ecotone between habitats only a single species is recognized, N. acunhae (see Ryan 2008, Bird Conservation International 18: 30–39). Genetic analysis suggests that small and large-billed populations have evolved independently at each island (see Ryan et al. 2007, Science 315: 1420-1423 for details), although the phylogenetic signal may have been obscured by recent hybridisation. Recent fieldwork in 2009, following similar sampling in 1989 and 1999, suggests that the range of bunting phenotypes on Inaccessible Island has remained constant over the last 20 years, despite hybridisation. Samples collected in 2007 and 2009 will be used to further investigate the evolution of these birds using an array of genetic tools (see project: Unravelling the genetics of ecological speciation).

Unravelling the genetics of ecological speciation: adaptive genomics of two avian radiations

Research team: Martim Pinheiro de Melo (project leader) & Peter Ryan

Collaborators: CIBIO (Portugal), Lund University (Sweden), Sheffield University (UK) and the University of Pretoria.

Understanding the genetic bases of adaptive divergence and speciation will be the next major challenge in evolutionary biology. We are approaching this problem by investigating two cases of adaptive radiation in finches. The study models have been chosen for their simplicity and because molecular and ecological data indicate that selection has played a major role in these radiations. We are sampling a large number of unlinked markers across the genome (including c. 40 microsatellite loci and a microarray able to analyse c. 18,000 genes) in order to distinguish between neutral and selected loci. The former will be used to infer robust phylogenetic and demographic histories, and the later to identify regions underlying phenotypic variation. As we are particularly interested in identifying regions underlying bill evolution, we will assess if genes known to be responsible for bill development in other species play the same role here. We shall use population and functional genomics, firstly to identify regions under selection and, secondly, to determine the exact genes responsible for adaptation and ultimately speciation. The project aims to launch a long-term international collaborative research programme on the genetics of ecological speciation, using birds as models. It is a collaboration with the following institutions: CIBIO (Portugal), Lund University (Sweden), Sheffield University (UK) and the University of Pretoria.

Phylogenetic relationships of supra-generic taxa in the order Galliformes from organismal and molecular perspectives: effects of partitioning and combining data and of missing data and choice of root.

Research team: Tim Crowe

Collaborators: Paulette Bloomer, Rebecca Kimball, Edward Braun, Ettore Randi & Jeff Groth.

Phylogenetic relationships among 92 species representing all supra-generic taxa in the chicken-like birds of the Order Galliformes are inferred from organismal (osteology, behaviour, integument, reproductive biology) and molecular (allozymes, amino acid and DNA sequences) data. Traditional groupings (partridges, quails and pheasants) are shown to be polyphyletic. With the exception of the New World quails (Odontophoridae), there is strong congruence between phylogenies derived from separate and combined data. Molecular analyses place them near the base of the phylogeny, whereas organismal analyses place them as a terminal taxon. If the analysis is rooted on the ostrich-like birds, the Cracidae (a largely South American group) is more closely related to ducks and geese (anseriforms) than to any group of galliforms. Missing data (which was largely molecular) undermined the terminal structure of phylogenies, but was useful in resolving basal branching patterns.

Phylogenetics of Francolins from organismal and molecular perspectives

Research team: Tim Crowe (project leader) & Dr Paulette Bloomer, University of Pretoria

The phylogenetics of francolins was investigated from organismal and molecular perspectives. the group is not monophyletic. Quail-like francolins (e.g. Redwing, Greywing, Shelley's, Coqui, etc.) are more closely related to Asiatic phasianids and partridge-like species (e.g. Cape, Swainson's, Natal, Red-billed, etc.) are closer to Eurasian partridges. It was found that there is good congruence between results of separate analyses of molecular and organsimal data. However, best resolution and phylogenetic structure were obtained through analyses of combined data.