Life on the edge: A new bioinformatic toolbox to conserve wildlife populations under threat from global change

Global change threatens biodiversity, with many species unable to respond fast enough to changing conditions due to rapid climate change and anthropogenic impacts. Population declines are our early warning signals for larger scale declines in species, so assessing the adaptive capacity of populations within species and quantifying their vulnerability under future global change remains a priority for biodiversity research.

This is the focus of my recently funded project, “Life on the edge: A new bioinformatic toolbox to conserve wildlife populations under threat from global change”, for which I obtained a 3 year grant from sDiv, the synthesis centre of iDiv (German Centre for Integrative Biodiversity Research). In this project I’ll integrate ecological (traits, species distribution models), environmental (climate change forecasts, landscape connectivity) and genome-wide molecular data (neutral and adaptive diversity) for populations across multiple species in a novel, automated and extendable climate change vulnerability assessment framework.

The work is inspired by this excellent publication, and includes the following collaborators:

Orly Razgour, University of Exeter, UK
Renske Onstein, iDiv, Leipzig, Germany
Malin Pinsky, Rutgers University, NJ, USA
Hjalmar Kühl, MPI-EVA and iDiv, Leipzig, Germany
Sebastian Steinfartz, University of Leipzig, Germany

I’ll post updates on this work as it develops, it will integrate over 100 species datasets across Africa and Europe, and involve a lot of automating complex code from a variety of different sources. There will be a GitHub site coming soon to act as a central repository for the code.

Recent clinal variation and genetic connectivity in chimpanzees across Africa

Quick update to disseminate a paper I have been working on with Jack Lester (Max Planck Institute of Evolutionary Anthopology) amongst others in Leipzig, now published in Nature Communications Biology here. Drawing on many years of fecal sampling from across the entire range of chimpanzees (>5300 samples from 21 countries), and building the largest microsatellite dataset for the species to date, we show that chimpanzees demonstrate a pattern of isolation by distance, and that the proposed riverine and arid barriers separating subspecies show signals of recent genetic permeability. We also find strong signals of differentiation at the local scale, linked to anthropogenic pressure, highlighting the need to safeguard critical genetic diversity to mitigate the effects of future habitat fragmentation and population isolation.

Looking for a PhD student: Harnessing the power of RADseq data to achieve a more mechanistic understanding of rapid evolution

Details on how to apply (deadline 27th January 2021)

As part of a collaborative project led by Isabell Hensen, Christoph Rosche, Renske Onstein, Walter Durka and myself, we are looking for a PhD student to study rapid evolution using genomic data of a wide-spread invasive plant species. This project is in cooperation with the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig. Please forward this to interested parties!

This integrative project will apply RADseq analyses to identify molecular mechanisms of rapid evolution in native and non-native Conyza canadensis populations. Landscape genomics will unravel adaptive and non-adaptive drivers of the global genomic structure of this cosmopolitan weed. Available common garden data will allow studying genomic associations for intraspecific trait variation for phenotypic (competitive ability) and metabolomic data (root exudate profiles). The project will be supervised by the iDiv members Isabell Hensen (MLU Halle), Walter Durka (UFZ Halle) and Renske E. Onstein (iDiv Leipzig) and myself.

• Performing population genomic lab work and data analyses
• Publishing scientific papers in peer-reviewed journals
• Presenting results at national and international conferences
• Interactions with molecular and evolutionary ecologist at MLU, UFZ and iDiv
• Travelling for interactions with collaborators from the University of Montana
• Active participation in the yDiv graduate school
• Qualification goal: PhD in population genomics

• M.Sc. or equivalent scientific university degree in a project-related field (e. g., population genetics, plant
genomics, population ecology, plant ecology and evolution, invasion biology)
• Statistical skills, experience with R
• Expertise and experience in population genetics are advantageous
• Experience in working with data pipelines is also advantageous

Please get in touch if you have any questions!

Chimpanzees show greater behavioural and cultural diversity in more variable environments

Chimpanzees crossing savannah habitat in Bafing, Mali, a location with high seasonality that supports high behavioural diversity. © PanAf/MPI-EVA

We recently published a paper in Nature Communications demonstrating that both historical and recent variation in ecological and environmental conditions are associated with larger behavioural repertoires in wild chimpanzees. The work was co-led by my colleagues Dr. Ammie Kalan and Dr. Hjalmar Kuehl, part of the Pan African Programme: The Cultured Chimpanzee. The paper is available open access here, and you can read a full press release with further details from the Max Planck Institute here. Enjoy!

New paper on Hyperolius mitchelli and H. rubrovermiculatus out now!

A new paper, led by Beryl Akoth Bwong (formerly a colleague of mine in University of Basel but now at the National Museums of Kenya) is out now! In this work we investigated the phylogeography and systematics of Hyperolius mitchelli, a widespread species in Tanzania and Malawi, along with its closest relatives (including H. rubrovermiculatus from Kenya and H. stictus from Mozambique). This group is an interesting species complex, and there still remain several undescribed evolutionary lineages that we documented to expand knowledge of this group for their future conservation.

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Sampling locations across East Africa

Being able to identify species properly is one of the fundamental requirements of protecting them, but this is not always so straightforward, even when you have one right there in front of you along with a species identification guide. A particular problem with this group is that morphological and colour variation is extremely high, even within a single species, as is the case for most Hyperoliidae (African sedge and bush frogs). This means that we need to employ additional methods to determine species identities.

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Phylogenetic reconstruction of the species complex, note the placement of H. cf. mitchelli from northern Tanzania within H. rubrovermiculatus, and the 3 unique lineages within H. mitchelli.

In this work we did exactly this, combining genetics, morphology and acoustic analyses to analyse populations from across all three species ranges. We found several unique lineages within H. mitchelli, and also that populations in northern Tanzania (previously assumed to be H. mitchelli) are actually a geographically isolated lineage of the Kenyan species, H. rubrovermiculatus. This simultaneously extends the known geographic range of  H. rubrovermiculatus (listed as Endangered by the IUCN) and reduces the known geographic range of H mitchelli (listed as Least Concern by the IUCN). With this work we further refine our knowledge of species identities, genetic composition and geographic ranges, which will all ultimately influence how they are categorised by the IUCN redlist in the future, and potentially help to better conserve important habitats for species.

The full article is available from the African Journal of Herpetology here

Colour vision in primates closely linked to palm fruit colours

Our new paper on primate vision in relation to conspicuous fruit colours is out! See press release below, work led by Renske Onstein!

(Press release by iDiv (Kati Kietzmann)

The evolution of colour vision might be closely linked to the availability of food. Researchers from the German Centre for Integrative Biodiversity Research (iDiv), Leipzig University (UL), and the University of Amsterdam (UvA) found that colour vision in African primate species, which is similar to that of humans, is related to the spatial distribution of palm fruit colours. The results of their study have been published in Proceedings of the Royal Society B. They shed new light on the evolution of primates.

In our retina, three kinds of receptors are responsible for the perception of basic colours: red, green and blue. The same holds true for many primate species – in contrast to all other mammals. For nocturnal species, the ability to distinguish different colours would not provide a significant advantage. It is therefore highly probable that so-called trichromatic vision developed in diurnal primates. In addition to greens and blues, they can also distinguish shades of red, making it easier to detect coloured fruit. This could provide a competitive advantage over other fruit-eating animals that cannot distinguish red from green. While this idea had been tested experimentally in a few species, it remained largely unexplored on a larger scale.

A team of researchers from iDiv, UL and UvA has now shown that trichromatic vision in primates is strongly linked to the availability of conspicuous, red palm fruits. Their research involved analysing data on the colour vision and distribution of more than 400 primate species as well as fruit colour data for over 1700 palm species. The result was clear: trichromatic vision in primates is most common in African countries with a high proportion of palm species with very colourful, conspicuous fruits.

This relationship is a win-win situation, benefiting both primates and palms: while primates rely on palm fruits as their primary food source, they are also important seed dispersers in tropical forests, particularly for large fruits. The research shows that the number of diurnal, fruit-eating primates in Africa increases with the proportion of conspicuous palm fruits, with a peak in subtropical regions. The results suggest that the effects of palm fruits on primates are strongest in the transition zones of arid to subtropical regions, where competition for food is also high. For the African primates, the ability to see several colours is thus an advantage when foraging. Palms, in turn, evolved colourful fruits that could be easily spotted by the primates, thus helping to disperse their seed.

The researchers did not only analyse data from the African continent, but also from Asia and the Americas. “Interestingly, in the Americas and Asia some primate species have trichromatic vision, whereas others do not. Here, we did not identify a relationship between colour vision and the proportion of conspicuous palm fruits,” said first author Dr Renske Onstein from iDiv and UL. Furthermore, most primates in the Americas prefer palm fruits with non-conspicuous colours. By contrast, many trichromatic primates in Asia have no interest whatsoever in a fruit’s colour – they enjoy feeding on large amounts of fruit in general.

“In Asia and the Americas, birds and bats could play a more important role as seed dispersers than primates,” explained Dr Daniel Kissling from UvA, senior author of the study. “In contrast, there are relatively few frugivorous birds on the African continent, so palm species may rely more on primates as seed dispersers than other fruit-eating animals.” The analyses show that palm species in Africa are dominated by those with conspicuous fruits, whereas the fruits of American species tend to be more inconspicuous.

Many primate species are now threatened with extinction due to rapid habitat loss and global changes. This may have cascading effects, especially when some plant species rely on primates as their primary seed dispersers. Thus, conservation efforts should also take plant-animal interactions and fruit-colour diversity into account as this is crucial for maintaining tropical biodiversity.


Dr Renske Onstein
Head of the junior research group Evolution and Adaptation
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
Phone: +49 341 9733 -129

Chimpanzee (<em>Pan troglodytes</em>) feeding on a wild date palm (<em>Phoenix reclinata</em>). (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)

Chimpanzee (Pan troglodytes) feeding on a wild date palm (Phoenix reclinata). (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)

Primates rely on palm fruits as their primary food source. (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)

Primates rely on palm fruits as their primary food source. (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)

But they are also important seed dispersers in tropical forests, particularly for large fruits.&nbsp; (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)

But they are also important seed dispersers in tropical forests, particularly for large fruits.  (Picture: M. McLennan / Bulindi Chimpanzee & Community Project)


ATBC 2019 Madagascar

I recently got back from a trip to the Indian Ocean with my family where I travelled to Madagascar to attend the 56th annual meeting of the Association for Tropical Biology and Conservation. It was my first time in Madagascar, one of the world’s foremost biodiversity hotspots, my forest experience at a ATBC conference with lots of tropical diversity and conservation (as you would expect from the name…).

I co-organised a symposium there with Renske Onstein entitled “Broad-scale determinants of tropical diversification and community assembly”, and we had some great speakers who spoke about micro- and macro-evolution across the neotropics, Africa and Australia. Many thanks to Dan Rosauer, Andrea Paz, Flavia Pezzini, Lucia Lohman, Caroline Lehmann and Paul Fine for agreeing to speak about their interesting work in our symposium and making it a huge success. Also thanks to the conference organisers for a fantastically organised programme!

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Sexual colour dimorphism drives evolutionary radiations in African reed frogs

Interested in evolutionary radiations and colourful African frogs? Then take a look at this important new paper published by Dan Portik and collaborators from 16 different countries across Africa, Europe and the US. 

Sexual dichromatism (when females and males show striking colour differences) is potentially thought to drive rapid evolutionary radiations in some groups. Though it is quite rare in amphibians, present in only around 2% of species – in Hyperoliidae (African reed frogs) it is particularly prevalent. Unlike most other vertebrates, hyperoliid females tend to be the ones showing off their ornate colours, whereas the males stay as low-key greens or browns. Until now, we have been unsure of the origins of this very conspicuous colour dimorphism, or if it is even associated with rapid bursts of evolution in frogs.

Illustration of (a) several Hyperolius species in the predominately sexually dichromatic Clade 1 and (b) several Hyperolius species in Clade 2 that exhibit multiple transitions to secondary monochromatism. Males are positioned in the top rows, with females below, and the phylogenetic relationships among species are depicted (though not all taxa have been included) Photo credits: Daniel Portik, Jos Kielgast, Bryan Stuart, Andrew Stanbridge.

Using years of collaborative Pan-African field sampling, Dan developed over 1000 sequence capture loci for a large proportion of the African Hyperoliidae (254 samples from 12 genera) and built a new high-resolution phylogeny to investigate the relationships between species. He then used this to show that dichromatism evolved once, followed by multiple reversals to monochromatism in some species, and demonstrated that increased net diversification rates are shown in sexually dichromatic species – on average twice the rates shown by monochromatic species!

Though sexual dichromatism is clearly linked to rapid evolution in hyperoliids, its exact function remains unclear, and so it presents a very interesting and novel model system for future research into how sexual selection and natural selection may interact across evolutionary timescales.

How missing data and degraded DNA samples may affect phylogenetic reconstructions using RAD-seq datasets

Our new paper is out in Zoologica Scripta which looks at the causes and impacts of missing data using a RAD-seq dataset for an African frog (Afrixalus fornasini). You can read the full work here, but below is the abstract:

Restriction site‐associated DNA sequencing (RADseq) has emerged as a useful tool in systematics and population genomics. A common feature of RADseq data sets is that they contain missing data that arise from multiple sources including genealogical sampling bias, assembly methodology and sequencing error. Many RADseq studies have demonstrated that allowing sites (single nucleotide polymorphisms, SNPs) with missing data can increase support for phylogenetic hypotheses. Two non‐mutually exclusive explanations for this observation are that (a) larger data sets contain more phylogenetic information; and (b) excluding missing data disproportionally removes sites with the highest mutation rates, causing the exclusion of characters that are likely variable and informative. Using a RADseq data set derived from the East African banana frog, Afrixalus fornasini (up to 1.1 million SNPs), we found that missing data thresholds were positively correlated with the proportion of parsimony‐informative sites and mean branch support. Using three proxies for estimating site‐specific rate, we found that the most conservative missing data strategies excluded rapidly evolving sites, with four‐state sites present only when allowing ≥60% missing data per SNP. Topological similarity among estimated phylogenies was highest for the data sets with ≥60% missing data per SNP. Our results suggest that several desirable phylogenetic qualities were observed when allowing ≥60% missing data per SNP. However, at the highest missing data thresholds (80% and 90% missing data per SNP), we observed differences in performance between high‐ and mixed‐weight DNA extraction samples, which may indicate there are trade‐offs to consider when using degraded genomic template with RADseq protocols.

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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.

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