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Testing Tropical Diversity Hypothesis Using a Non-Invasive Approach

The primary objective of this study is to compare patterns of population genetic variation in a suite of central African forest duiker species (genus Cephalophus) and use these data to test alternative hypotheses of tropical diversification in Central African rainforests. Mechanisms of species diversification have been a subject of intense debate and interest in rainforest ecosystems (Haffer, 1997; Patton and da Silva, 1998). With the advent of PCR-based methods, geo-referenced genetic data can provide exciting insights into the historical and ecological processes underlying patterns of rainforest diversification (Moritz et al., 2000). Whilst much of the preceding work has been conducted in the Amazonian and Australian tropics (e.g. da Silva and Patton, 1993; Patton et al., 1994; Joseph et al., 1995; Patton and da Silva, 1998; Schneider et al., 1999), data on central African rainforest taxa remain sparse, largely due to the difficulty of obtaining a sufficient number of samples of known origin to test geographically explicit hypotheses.

In order to overcome this difficulty, this project makes extensive use of a non-invasive strategy to obtain DNA from geo-referenced feces sampled from artiodactyl communities across central Africa. Artiodactyls within the duiker genus Cephalophus were selected as target taxa for this study due to their high proportional abundance, remarkable species richness and strong association with forested habitats. Target taxa within central African forests include the following species: C. monticola, C. callipygus, C. dorsalis, C. silvicultor, C. nigrifrons, C. leucogaster, and C. ogilbyi. Additional focal taxa outside this group include the sitatunga Tragelaphus spekei, the bushbuck T. scriptus, the pygmy antelope Neotragus batesi and the water chevrotain Hyemoschus aquaticus.

Within central African rainforests, up to seven or more duiker species can occur in sympatry (Kingdon, 1997). However, many if not all, are impossible to discriminate on the basis of the appearance of their feces (Bowkett et al., 2008; van Vliet et al., 2008). Therefore, the first objective of this study was to develop a molecular diagnostic for differentiating tropical forest artiodactyls from their fecal pellets. The mitochondrial and nuclear microsatellite data obtained from these fecal samples will then be used to test three important hypotheses of tropical forest species diversification: (1) the Pleistocene forest refuge hypothesis of Haffer (1969), (2) the riverine barrier hypothesis invoked by Wallace (1849) and (3) the ecological gradient model of Endler (1977, 1982).  The specific aims of this study are as follows:

Aim 1: Design a suitable molecular diagnostic from a set of known reference samples in order to identify individual fecal samples to species level. A molecular diagnostic capable of recovering species identity will not only provide an important first step in identifying species for further genetic analysis but also yield valuable information on the geographic distributions and habitat associations of artiodactyl species inhabiting central African forests.

Aim 2: Compare geographic patterns of mitochondrial and nuclear variation across duiker species and use these data to test the potential impacts of Pleistocene forest refugia, riverine barriers and forest-savannah gradients in shaping patterns of evolutionary diversification. For the refuge model, tests of population differentiation and demographic change will be used to evaluate genetic signatures of historical population fragmentation and expansion. In the case of riverine barriers, cross-bank comparisons across one or more major rivers (Ogooué, Sanaga) will be used to test the hypothesis that rivers constitute major barriers to gene flow. Lastly, the impact of ecological gradients will be assessed by comparing population and individual-levels of genetic differentiation along a regional and local forest-savanna/mosaic gradient, respectively.


Bowkett A.E., Plowman A.B., Stevens J.R., Davenport T.R.B. and Jansen van Vuuren B.J. (2008). Genetic testing of dung identification for antelope surveys in the Udzungwa Mountains, Tanzania. Conservation Genetics 10: 251-255.
da Silva M.N.F. and Patton J.L. (1993) Patterns of evolutionary divergence in arboreal Amazonian echimyid rodents: the perspective of mtDNA sequence variation. Molecular Phylogenetics and Evolution 2: 243-255.
Endler J.A. (1977) Geographic variation, speciation and clines. Monographs in Population Biology 10. Princeton University Press, Princeton, NJ.
Endler J. A. (1982) Pleistocene forest refuges: fact or fancy? In: Biological diversification in the tropics (ed. Prance G.T.) pp. 641-657. Columbia University Press, New York.
Haffer J. (1969) Speciation in Amazonian forest birds. Science 165: 131-137.
Haffer J. (1997) Alternative models of vertebrate speciation in Amazonia: an overview. Biodiversity and Conservation 6: 451-476.
Joseph L., Moritz C. and Hugall A. (1995) Molecular support for vicariance as a source of diversity in rainforests. Proceedings of the Royal Society of London Series B 260: 177-182.
Kingdon J. (1995) The Kingdon Field Guide to African Mammals. Academic Press Ltd., London.
Moritz C., Patton J.L., Schneider C.J. and Smith T.B. (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review in Ecology and Systematics 31: 533-563.
Patton J.L., da Silva M.N.F. and Malcom J.R. (1994) Gene genealogy and differentiation among arboreal spiny rats (Rodentia: Echimyidae) of the Amazon basin: a test of the riverine barrier hypothesis. Evolution 48: 1314-1323.
Patton J.L. and da Silva M.N.F. (1998) Rivers, refuges and ridges. In: Endless forms: species and speciation (eds. D.J. Howard and Berlocher S.H.) pp. 202-216. Oxford University Press, New York.
Schneider C.J., Smith T.B., Larison B. and Moritz C. (1999) A test of alternative models of diversification in tropical rainforests: ecological gradients vs. rainforest refugia. Proc. Natl. Acad. Sci. USA 96: 13869-13873. 
Van Vliet N., Zundal S., Miguel C., Taberlet P. and Nasi R. (2008). Distinguishing dung from blue, red and yellow-backed duikers through noninvasive genetic techniques. African Journal of  Ecology 46: 411-417.
Wallace A.R. (1849) On the monkeys of the Amazon. Proceedings of the Zoological Society of London 20: 107-110.



  • Nicola M. Anthony
  • UNO, Dept. of Biological Sciences
  • 2000 Lakeshore Dr, New Orleans LA 70148