Outreach article: The story is in the genes

Volker Hahn, the Head of the Media and Communication team at iDiv, wrote an outreach article for the general public, as part of the online magazine of the University of Leipzig, about our work on Madagascar. It features both me and PhD student Laura Mendez and her adventures in the field, the lab, and behind the computer. The article also describes some of the future ideas and directions of our work. It’s in German.

Along with the article, Gabriele Rada made a short video about the Madagascar work, using our video footage from Madagascar. Watch the video here. And do not forget to also watch our other Madagascar video using megafauna animal animations by TRICKLABOR.

Looking for a PhD student!

I am looking for a PhD student to work on seed dispersal, connectivity and genomics of palms with megafaunal fruits on Madagascar – the position can be started as soon as possible, and the student will be located at the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, Germany.

Applications are accepted until 30th June 2018. To apply, see here: https://www.idiv.de/about_idiv/career.html 

Or download the advertisement here.

A bit more background….

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Extinct megafauna on Madagascar, image by VELIZAR SIMEONOVSKI

Madagascar harbours exceptional biodiversity, but this tropical hotspot also faces increasing threat from human activities and climate change. Plants with large, ‘megafaunal’ fruits are common across the flora of Madagascar, especially within the palm (Arecaceae) family. However, Pleistocene extinctions of large-bodied ‘megafaunal’ fruit-eating and seed-dispersing animals (such as giant lemurs) may have hindered the dispersal of taxa with megafaunal fruits. In this project we aim to investigate the micro- and macroevolutionary consequences of dispersal limitation for megafaunal-fruited palms on Madagascar, using a comparative framework. Specifically, we aim to (i) identify genomic signatures of dispersal limitation in megafaunal-fruited palm populations, (ii) reconstruct demographic history and identify historical genetic bottlenecks in these species, and (iii) evaluate whether these species may be adapting to dispersal by smaller-bodied frugivores, by evolving smaller fruits with smaller seeds. This project integrates the fields of plant evolution, phylogeography, and plant-frugivore interaction ecology. It will be in collaboration with researchers from Kew Botanical Gardens, UK (Dr. Bill Baker), Aarhus University, Denmark (Dr. Wolf Eiserhardt), the University of Amsterdam, the Netherlands (Dr. Daniel Kissling) and Botanic Garden of the Ruhr-University Bochum, Germany (Dr. Wolfgang Stuppy), among others.

Job description:
  • collecting genetic samples from palm populations on Madagascar, and measuring their functional traits;
  • identifying Malagasy frugivore communities and their functional traits;
  • using novel genomic techniques (e.g. RAD sequencing) to infer connectivity, demographic history and phylogeographical patterns;
  • writing and publishing of scientific papers in peer-reviewed journals;
  • presentation of results at international conferences;
  • participation in iDiv’s PhD training program yDiv.

Requirements:
Applicants should hold a Master’s or equivalent degree in a related field of research (e.g. ecology, (molecular) biology, genetics, phylogenetics, phylogeography). The successful candidate should be innovative, able to work on his or her own initiative, and willing to spend several months in the field (Madagascar). Therefore prior experience with tropical fieldwork and basic living conditions is advantageous. Furthermore, the successful candidate should have prior experience using molecular techniques, preferably with bioinformatics for large genetic/genomic datasets. An interest in acquiring additional necessary skills (e.g. programming) for handling and statistically analyzing large datasets is essential. Candidates should be team-oriented and have strong organizational skills, in order to manage this collaborative research project within an international consortium. Excellent English communication skills (speaking and writing) are required. We seek candidates with an independent mind and the ambition to publish in internationally leading journals.

Applications are accepted until 30th June 2018, the applicant is expected to start as soon as possible, but latest by September 2018.

For queries on the application process, please contact Dr. Nicole Sachmerda-Schulz (nicole.sachmerda-schulz@idiv.de); for research project questions, contact Dr. Renske Onstein (onsteinre@gmail.com).

Proteaceae and their success in open habitats

geb-cover-onstein-et-al-leucospermum-cordifolium

Leucospermum erubescens

In a recent study, published in the journal Global Ecology and Biogeography, we investigate the evolution of leaf morphologies and climatic niches in the Proteaceae family. Proteaceae is a Southern 20131216143659639-page-001Hemisphere family famous especially in Australia and South Africa for their impressive flowers and leaves. They are also tasty – the macademia nut belongs to the Proteaceae as well. Species in the Proteaceae family occur in all kinds of habitats, from montane forests to dry heathlands to tropical rainforests. During their evolution over millions of years, they managed to adapt to these variable and extreme habitats and climates, and their leaves may have helped them doing so. In this study we test whether open (e.g. mediterranean) and closed (e.g. tropical rainforest) habitats have selected for divergent leaf designs. We also show that the combination of certain leaf traits (e.g. small, sclerophyllous leaves with many teeth) in interaction with certain climatic niches (e.g. warm, dry, mediterranean) may increase diversification rates. This could explain some of the spectacular radiations within the family, for example inbanksia-speciosa-9_10-566x800 genus Banksia in Australia, or the Protea in Africa. Last, we show that there is more stochastic evolution of traits and niches in open habitats, which may explain some of the extreme forms and ‘misfits’ we find here. This “disparification” maybe even led to the process of reproductive isolation and speciation, roupala-longipetiolata-4_6-mtvia ecological divergence, and the ~1700 species of Proteaceae we find on Earth.

Onstein, R.E., Jordan, G.J., Sauquet, H., Weston, P.H., Bouchenak-Khelladi, Y., Carpenter, R.J., Linder, H.P. (2016). “Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats.” Global Ecology and Biogeography 25 (10):1239–1251. doi: 10.1111/geb.12481

 

A week with Shipley

 

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Wageningen University, credit: JD Santillana-Ortiz

Last week I traveled back to my scientific roots (Wageningen University) to participate in a course on Structural Equation Modeling (SEM) given by Bill Shipley (he is particularly well known from his book on ‘Cause and Correlation in Biology‘). Structural Equation Models can be used to evaluate the sequence of variables affecting each other, and whether the underlying data supports such a sequence of events (also called path-models). For example – ecosystem functions (e.g. productivity and decomposition) can be affected by the biomass of the vegetation, and this can be affected again by the age of the plot (e.g. during succession) (Lohbeck et al. 2015).

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some notes…

As an evolutionary ecologist I was a  bit of a misfit in the group. The group was dominated by Dutch PhD students and professors working in ecology (e.g. functional ecology, community assembly, soil science). They often collect data from plots; data which fit perfectly well in a structural equation model. My data did not – for a couple of reasons. My ‘plots’ are fossil assemblages (species richness = count data, problem 1), collected during the Cenozoic (different time scales, problem 2) and the variables we have are often not assemblage-specific but biased by time, and not normally distributed (e.g. CO2 concentration, temperature, latitude). On the positive side – I have a large sample size (N=666), which is necessary to have enough power to run these SEMs. So how can I test what factors directly and indirectly affect biodiversity (species richness)?

The solution. There is a solution. If your data is spatially, or phylogenetically biased, if your variables are not normally distributed, if you deal with binary/categorical/count data, if you have a nested design… The solution is the d-separation test. (d-sep cannot deal with ‘latent’ variables, e.g. unmeasured variables which may be important for the model).

d-separation in 6 steps:

  1. your hypothetical model (DAG: “Directed Acyclic Graph” avoid feedback loops in the model!) (for simplicity: A<- B <- C)
  2. write down each pair not connected by an arrow (in our example only AC)
  3. causal parents of these? (i.e. causal parent of A = B and of B = C. In our example of AC there is just one causal parent: B)
  4. run a suitable linear model/generalized linear model/PGLS/mixed model in which you test the effect of your pair variables, conditioned on the parent variables, in our example, of C on A conditioned on B (A ~ B + C)
  5. sum the probabilities (p values) of the slope coefficients of the regressions (in this case only one regression model was run, and we asses the coefficient of C and it’s p-value)
  6. calculate the C-statistic: -2 * ln (the sum calculated in step 5) and compare this to a Chi-square distribution. The degrees of freedom are calculated by 2* the number of regressions run (in our case 2 degrees of freedom). If p>0.05, you cannot reject you hypothesized model. If p<0.05 your data do not support the model.

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    All analyses can be performed in R using packages ggm and lavaan. credit: JD Santillana-Ortiz

Thanks to the d-separation test we, evolutionary biologist, can still test for causal relationships in our data, even if these data are far from ‘perfect’ or complete. It provides great potential for the field of phylogenetic comparative methods. But how exactly I’m not sure yet….

Reference

Madelon Lohbeck, Lourens Poorter, Miguel Martínez-Ramos, and Frans Bongers 2015. Biomass is the main driver of changes in ecosystem process rates during tropical forest succession. Ecology 96:1242–1252. http://dx.doi.org/10.1890/14-0472.1

Towards the end of a PhD…

I’m about to finisP1040954h my PhD. If we believe the PhD comics (http://phdcomics.com/comics.php) this comes with a lot of stress. It seems so simple: 4 years of research, testing hypotheses, collecting data, and write it down. The shorter the better – as long as all data is presented, in a cutting-edge, life-changing story. Why then, is finishing often so difficult? Perhaps it has to do with the perspective of a life after the PhD. Because is there such a thing, a life after the PhD? Does handing in the thesis come with a blue sky, birds singing, the ultimate feeling of happiness? Or will there be the black hole? Secretly, I hope there will be birds and other happy animals, but I’m afraid finishing is so difficult because of the uncertainty of what will be next. Especially in Academia there may not be a ‘next’, or, if there is, you’ll have to fight for it, and even harder than during the PhD. So, I decided to reduce the stress of finishing – it won’t help, and there is no perspective of a stress-less life afterwards, so better start early. How to do it? Spend enough time doing other things than science, go out in nature, or a club, take enough sleep, and most importantly, realize that the piece of paper you’re about to hand in will be read by, on average, four people, and that communicating a passionate work should be a hobby, not a job.