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.




Evolution2018 and a new Molecular Ecology paper

I recently came back from Evolution2018 in Montpellier, one of the largest gatherings of evolutionary biologists in the world to date (almost 3000 delegates from over 60 countries).  There I presented some upcoming work using multi-species RAD-seq datasets to test competing diversification processes in tropical biodiversity hotspots. Although the last decades of DNA-based research have vastly improved our knowledge of biodiversity patterns in poorly known tropical regions we lacked the high resolution genomic data needed to uncover the processes which are responsible for these patterns.

With high-throughput genomic data, our work tested if areas of forest which have remained stable over long periods of time (millions of years) are responsible for the diversification of amphibian populations within several co-distributed species, or if these diversification events can be attributed to alternative processes (e.g. mountain barriers, river barriers, ecological gradients or human influence).

This paper has just been accepted in Molecular Ecology, I will post an update when it is properly published as a PDF. In the meantime a snippet of this work is shown below in the attached poster, and you can find the accepted manuscript (not yet typeset) here.


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Dynamic aspects of Chimpanzee diversification across Africa using paleoclimate and genomic data


I’m pleased to announce that I will soon relocate to Leipzig in Germany where I will begin a 2 year postdoc position until September 2020. I’ll be working with in collaboration with iDiv (German Centre for Integrative Biodiversity Research), the Department of Primatology at the Max Planck Institute for Evolutionary Anthropology, and the Comparative Genomics Lab at the Institut Biologia Evolutiva, Universitat Pompeu Fabra (Barcelona).

My postdoc work will investigate the historical habitat connectivity and evolution of chimpanzee populations over the last 120,000 years using paleoclimate and genomic data. These data will provide novel information about the environmental and evolutionary processes affecting chimpanzee diversification. In turn this helps us understand their complex genetic and cultural diversity, simultaneously providing essential conservation data for our closest living relative.

This project links with the existing PanAf project run by my new colleagues, but will bring a new paleoclimatic perspective along with contributing some valuable conservation genomic information for the future protection of African biodiversity hotspots. More to follow soon!


Amnirana biogeography published in Molecular Phylogenetics and Evolution

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Fig. 1. Amnirana dated phylogeny and major biogeographic clusters

A paper I was involved in with lead author Greg Jongsma (Florida Museum of Natural History) concerning the diversity and biogeography of the genus Amnirana across sub-Saharan Africa was just published in MPE. The paper is the most comprehensive analysis of this group to date, including samples from 22 African countries.

Using a mixture of mitochondrial and nuclear genes, we reconstructed evolutionary relationships and divergence times for 10 of the 12 African species, finding that the African members of this group diverged from their Asian relatives around 37 million years ago. With our dense geographic sampling we discovered a wealth of cryptic diversity that is not yet recognised by current taxonomy (up to seven species! – sound familiar?)

Furthermore, by modelling biogeographic dispersal and vicariance events, we gained a sense of the evolution of this group and in particular the importance of forest refugia in the Lower and Upper Guinean Forests, which have acted as a major centre of diversification in Africa.

You can read the paper here.

Fig. 2. Sampling localities


Fig. 3. Amnirana lepus





Shimba Hills, Kenya – new amphibian checklist!

My colleague Beryl Bwong‘s paper just came out in the Journal of East African Natural History synthesising all current knowledge of amphibian diversity in the Shimba Hills National Reserve in Kenya based on existing data and comprehensive recent sampling. This is the first comprehensive amphibian checklist for the Shimba Hills, home to large populations of elephants and other game, including the only known population of Sable antelope in Kenya. The paper describes 30 amphibian species from Shimba Hills, placing it as one of the hotspots of amphibian diversity in Kenya. Although this special place is currently protected and reasonably well known, this work adds further evidence to its importance for biodiversity conservation in coastal Kenya.

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Fig. 1. Clockwise from top left – wetland and forest habitats within Shimba Hills, the endemic treefrog Hyperolius rubrovermiculatus and a recently re-discovered Brevicipitid frog which has not been observed in this reserve since 1961 (Callulina cf. kreffti.). Photos by Beryl Akoth Bwong.

I spent three years working together with Beryl at the University of Basel where we both completed our PhDs, and I’m happy to see this collaboration published and used for future safeguarding of the Shimba Hills. Congratulations Beryl, and for your ongoing and future work with the National Museums of Kenya!

You can access a PDF of the paper here.

Yunnan province, PR China

I just got back from China where I gave a couple of invited talks on my PhD research and recent projects in the Xishuangbanna Tropical Botanical Garden and the Kunming Institute of Botany. Though they are primarily botanical research institutes there are many ecologists and evolutionary biologists working there on many interesting questions about biodiversity changes over deep timescales which fits in nicely with my PhD work in Africa.

Though it was mainly work, I managed to visit some interesting sights – the Wangtinshu sky tree park, containing patches of ancient tropical forest up to a canopy height of 80m, and the Yunnan stone forest (Shilin), which contains huge monoliths of limestone from the Permian (up to 300 million years old!) that have been gradually eroded by rainfall to leave the impression of a forest made from stone. Many thanks to Prof. Xing Yaowu and his Biogeography and Ecology Group for hosting me and making me welcome on my first visit to this beautiful part of tropical China!

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Making better species distribution models with improved spatial sampling and taxonomic knowledge

I am pleased to report that a paper I am a co-author on has just been published in Molecular Phylogenetics and Evolution. The work shows how species distribution models (SDMs), also referred to as ecological niche models (ENMs) can be improved both by using a phylogenetic framework to refine taxonomic units and also increasing spatial data (Figs. 1 and 2). As usual this is a collaboration between scientists across the world (Europe, Africa and the US), and is the second MPE paper from the PhD of my colleague Gabriela Bittencourt-Silva – congratulations!

The paper is entitled “Impact of species delimitation and sampling on niche models and phylogeographical inference: A case study of the East African reed frog Hyperolius substriatus Ahl, 1931″ and is available online here.


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Fig. 1. Hyperolius substriatus samples used in this study (including samples from Lawson et al. 2013)
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Fig. 2. ‘Splitting’ or ‘lumping’ the species distribution models can have dramatic effects on spatial predictions. Using greater numbers of sampling points with more accurate taxonomic information (from multi gene mitochondrial and nuclear DNA analyses) provide clearer insights into lineage distributions and phylogeography.

Vulnerable East African amphibian species makes the front page!

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An image from work in our recent paper was selected as the cover of Diversity and Distributions – giving some much needed publicity to some of the beautiful amphibians and threatened forests that we research. This image is Afrixalus sylvaticus, listed as vulnerable on the IUCN red list and found in the Shimba hills of Kenya and forest patches of coastal Tanzania. Thanks to my colleague Beryl Akoth Bwong (now at National Museums of Kenya) for providing the nice photograph!

Evolution meeting 2017, Portland, Oregon

Portland logoThe Evolution meeting starts tomorrow! (as if you didn’t already know…).  Unfortunately I won’t be there in person, however my former PhD supervisor, Simon Loader (Natural History Museum London) will present a poster based on the paper I mentioned in the last post. I am sure Simon would be more than happy to talk about amphibian evolution and conservation in East Africa if you are interested. The poster is in the Comparative phylogeography poster session on Saturday 24th June.

Environmental correlates of phylogenetic endemism in amphibians and the conservation of refugia in the Coastal Forests of Eastern Africa

Our new paper is now available in early view in Diversity and Distributions here

With this work, my colleagues and I show how the inclusion of phylogenetic information for amphibians can help to identify priority areas for increased conservation efforts across Eastern Africa (Fig. 1).

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Fig. 1. The Coastal Forests of Eastern Africa (CFEA), with the adjacent Eastern Afromontane (EA) biodiversity hotspot

Although species are arguably the most fundamental measure of biodiversity on earth, they often contain high levels of genetic and morphological diversity across their geographic ranges. Even with common organisms we may often see striking patterns of  differentiation below the species level which is often overlooked, and is especially relevant for local and regional conservation efforts. So how can we incorporate this intra-specific diversity into conservation assessment and planning? When we have sufficient data, we can build a molecular phylogeny (an evolutionary tree) to resolve the relationships of species, and include the major lineages that make up each of these species. Combining the geographic distribution of each of these lineages and species with its corresponding branch length on the phylogeny we can highlight areas where large amounts of evolutionary history have accumulated (see Fig. 2).


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Fig. 2. A molecular phylogeny of species occurring in the coastal forests of Eastern Africa including species and intraspecific lineages, and a map of evolutionary history (PE) created by combining phylogenetic information with geographic data


This is the theoretical basis of our new paper, where we applied these methods for close to the full assemblage of coastal forest species across Tanzania and Kenya, leading to the compilation of the largest available genetic and geographic datasets to date. We hypothesised that many of the evolutionary hotspots in this region are important refugia for biodiversity in times of past climate change, and our results support the idea that long term climatic stability, benign current climate and topographic heterogeneity facilitate the persistence of evolutionary history (Fig. 4).

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Fig. 4. Model contributions in the best GLM to explain PE

Finally, by intersecting our maps with the current protected area network we established that much of the region’s evolutionary history is poorly protected, and several areas should be prioritised for conservation in the future (Fig. 5).

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Fig. 5. PE hotspots  intersected with the protected area network, showing the low levels of protection for much of the region’s amphibian evolutionary history