Testing competing diversification processes with genome-wide data in East Africa

Which environmental and ecological processes cause species to diversify into collections of isolated populations? Can we somehow capture and quantify these processes with empirical data to test long-standing hypotheses of evolution in highly biodiverse regions? Yes we can! Our new paper in Molecular Ecology does exactly this, using newly collected data for amphibians in the East African lowlands to test if forest refugia (i.e. long-term forest stability) are responsible for current diversity patterns, or if there have been other major drivers such as mountains, rivers or human impacts.

By integrating molecular dating, habitat stability modelling throughout the Pleistocene and genome-wide SNP analyses from high-throughput RAD-seq data we generated high resolution biodiversity patterns and quantified the evolutionary processes (e.g. isolation, migration, secondary contact and population expansions and contractions) shaping diversity across seven widespread species.

Fig. 1. High resolution phylogeographic structure across seven amphibian species in lowland East Africa, with different genetic clusters in each species marked on the map. A-C: Forest species, D-G: Generalist species

Although the phylogeographic structure of most amphibian species was remarkably similar (i.e. clear population structure across the geographic range, Fig. 1), we found that different processes were responsible for the diversity across species (Fig. 2). Contrary to our expectations only one out of three forest species showed signals that forest refugia were responsible for current diversity, with diversification also driven landscape barriers and ecological gradients between forest and savannah habitats. For all four generalist species however, the evidence pointed towards river barriers being extremely important for their recent diversification.

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Fig. 2. Best demographic models selected across species representing the tested evolutionary hypotheses based on genome-wide SNP data

Together, the results from the seven species demonstrate the complexity of diversification processes in tropical biodiversity hotspots, which vary between forest specialists and generalists but show that even common patterns in ecologically similar species can be caused by different processes. This work has broad significance for interpreting how biodiversity accumulates and persists in biodiversity hotspots, and should be useful to develop conservation strategies targeting multiple species, which can ultimately be upscaled to analyse whole community assemblages.

The paper is freely available open access, along with all data and analyses:

Barratt CD, Bwong BA, Jehle R, Liedtke HC, Nagel P, Onstein RE, Portik DM, Streicher JW, Loader SP. Vanishing refuge? Testing the forest refuge hypothesis in coastal East Africa using genomewide sequence data for seven amphibians. Mol Ecol. 2018; 27: 42894308. https://doi.org/10.1111/mec.148624308

For further reading a short press release can be found here.




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