Our response to Heymann & Fuzessy

It was the day before my maternity leave started that I received an invite from the journal Proceedings of the Royal Society B to submit a reply to the comment by Heymann & Fuzessy. They criticized some of the work my co-authors and I published in early 2020, on the relationship between palm fruit colours and the diversity of trichromatic vision (the ability to distinguish red and green) in primates. See here for the original publication. Luckily, the journal allowed me a bit of time to think about a response while nursing my baby.

The main issue that Heymann & Fuzessy raised, was that there is little natural history information on the dependence of primates on palm fruits, especially in Africa. Therefore, they considered the macroecological and macroevolutionary analyses we performed in our original article unreliable. In our response, we argue that our macro analyses, which show a strong relationship between the spatial and temporal diversity of trichromatic primates and that of conspicuous (e.g. reddish) palm fruits (see figure below), are indeed only one piece of the puzzle, and multiple lines of evidence are needed to further resolve the question whether primates evolved trichromatic vision as an adaptation to detect conspicuous fruits. This includes more natural history information – the dataset of Heymann & Fuzessy was limited and incomplete, especially for Africa – , network analyses, co-phylogenetic methods, and macro approaches as we did here, and perform these across a range of taxonomic plant groups that may be important food sources for primates. Good ones to start with could be Moraceae (figs and relatives), Melastomataceae, Annonaceae.

I hope to further address the question on whether palm fruits are important to explain the distribution and diversity of frugivores (including primates) in my future research.

Results from the original study, showing with structural equation models that the proportion of plants with conspicuous fruits in communities have a strong effect on species richness of day-active, frugivorous polymorphic and trichromatic primates in those same places.

Original publication: https://royalsocietypublishing.org/doi/10.1098/rspb.2019.2731

Comment: https://royalsocietypublishing.org/doi/10.1098/rspb.2020.1423

Reply: https://royalsocietypublishing.org/doi/10.1098/rspb.2020.2981

Looking for a PhD student to study population genomics of rapid evolution

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

As part of a collaborative project with Isabell Hensen and Christoph Rosche (among others) at the Martin Luther University Halle-Wittenberg (Germany), 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:

“Harnessing the power of RADseq data to achieve a more mechanistic understanding of rapid evolution”

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).

Tasks:
• 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

Requirements:
• 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

Get in touch if you have any questions!

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 technical assistant to join the group

Details on how to apply can be found here: 174_iDiv_Tech_Assistant_EA_REO_engl (deadline 12th of August 2020).

Technical assistant Evolution & Adaptation group at iDiv (Leipzig, Germany)

Limited until 30 September 2021. 100% of a full-time position. Salary: Entgeltgruppe 6 TV-L. Workplace: Leipzig.

The Evolution & Adaptation research group focuses on the interchange between (macro-) ecology and evolution, to understand the global distribution of genetic, taxonomic and functional diversity. We therefore generate genetic (genomic) data (e.g. from plants from Madagascar), and build databases of biodiversity data (such as functional traits) to investigate the link between genes and phenotype. Understanding these links is important for predicting how adaptable biodiversity is to current and future global change.

Tasks:

  • Combining (botanical) data sources (such as monographs and floras) to build databases for biodiversity data (using Access/PROTEUS or SQL)
  • Measuring functional plant traits from herbaria or fresh sample material
  • Collecting and cleaning plant species occurrence data from online data sources/herbaria
  • General laboratory organization and maintenance
  • Planning and conducting basic molecular techniques
  • Analysis of generated data and preparation of suitable presentations

Requirements:

  • Professional qualification as a Biological-Technical Assistant or an equivalent degree (e.g. BSc or MSc in Biology)
  • Hands-on experience with basic molecular techniques (e.g., DNA/RNA isolation, PCR, real-time PCR, gel electrophoresis) preferable
  • Experience in building databases preferable
  • Very good computer skills (MS Windows, MS Office, R, etc.)
  • Very good spoken and written English
  • Strong team player also able to work independently
  • Very well organized and reliable
  • Experience with working in interdisciplinary and international teams

For questions, contact me on onsteinre@gmail.com!

Looking for two PhD students to join iDiv!

Application details for both positions are now available – see below!

I am looking for two new PhD students to join the Evolution & Adaptation group at iDiv in Leipzig (Germany) from October 2020 onwards. The positions are fully funded (65% of a full time employment, Salary: Entgeltgruppe 13 TV-L) and for 3 + 1 years. There is a budget available for consumables to perform fieldwork, lab work, sequencing, visit conferences, herbaria, collaborators and take courses. The PhD students will become part of the yDiv graduate school. iDiv is a very international place to work in and learn about Biodiversity science more generally, with weekly seminars, and Leipzig is a lovely city with lots of green space and a cultural history to live in.

Below I briefly describe both projects. Feel free to get in touch (onsteinre@gmail.com) to find out more, if you are interested in applying to one of them:

1. Macroecology and macroevolution of plant – frugivore trait matching in the tropics

Application details available from here: 113_iDiv_P3_REO_engl and 112_general_announcement__4thFlexPoolcall_engl. Deadline for application: 10th July 2020.

Background: Mutualistic interactions between fleshy-fruited plants and frugivorous animals are prominent in tropical rainforests. These interactions are facilitated by the evolution of matching traits in both plants and frugivores, such as fruit size and frugivore gape width. Due to ongoing global change (e.g., defaunation) trait matching may have been distorted in certain places, such as highly disrupted regions, leading to co-extinction or rapid evolutionary change in plants/animals that relied on these locally extinct interaction partners. However, which places harbour such mismatches in traits is unknown. Furthermore, it is unclear when these interaction-relevant traits evolved, and whether they have influenced the past diversification dynamics of plants and frugivores. In this PhD project, we aim to understand the impact of frugivory-related plant and disperser trait origin and extinction on the macroecology and macroevolution of fruit-frugivore trait matching, by addressing three main questions: (1) Do frugivory-related plant and animal dispersal syndromes (i.e., sets of correlated traits) differ among biogeographical realms, or mainland/island systems? (2) Is the spatial distribution of frugivory-related plant traits matched by the corresponding animal disperser traits (e.g., fruit size ~ gape width), or are there mismatches due to Late Quaternary extinctions of particular mammalian, avian or reptilian functional groups? (3) Has there been trait matching or mismatching during particular geological time periods, leading to increased (co-)speciation or extinction? To answer these questions, we will focus on three plant clades that are keystone resources for frugivores in the tropics: Arecaceae (palms), Annonaceae (custard apples) and Fabaceae – Mimosoideae (legumes). Furthermore, we will match the plant data to frugivore data, primarily focusing on frugivorous birds and mammals. We will integrate phylogenetic, distribution and functional trait data for these clades and apply macroecological and macroevolutionary methods to answer the research questions. This project will shed light on the biogeography of plant-frugivore interactions to be able to identify places and lineages prone to ongoing (co-)extinctions of their interaction partners. This project is supervised by me, Ingolf Kühn, Isabell Hensen and Irene Bender, but the student will work with several more collaborators for the specific datasets and their expertise on the plant and animal clades.

Tasks:

  • Developing specific research questions and hypotheses within the scope of the project;
  • Assembling/cleaning plant and animal frugivory-related traits, phylogenetic and distribution data from online databases, literature, monographs and herbarium visits (partly already done);
  • Applying macroecological and macroevolutionary methods to test the specific hypotheses;
  • Writing and publishing scientific papers in peer-reviewed journals;
  • Presenting results at national and 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., biosystematics, (macro-)ecology, (macro-)evolution, environmental sciences). The successful candidate should be innovative, able to work on his or her own initiative, have expertise and experience in phylogenetics or working with phylogenetic data, interest and ability in handling spatial data and functional traits and strong statistical skills (in R). 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.

2. Adaptive evolution of plant-frugivore interactions on Madagascar

Application details available from here: 142_iDiv_PhD_Onstein_EA_engl. Deadline for application: 20th July 2020.

Background: 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-Holocene 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 molecular, micro- to macroevolutionary consequences of dispersal limitation in palms, specifically focusing on adaptive evolution of a megafaunal-fruited palm, Hyphaene coriacea, using a comparative framework of Madagascar (all megafauna extinct) and mainland Africa (where H. coriacea is still frequently dispersed by elephants). Specifically, we aim to (i) identify candidate genes for fruit and seed traits important for plant-frugivore interactions, (2) pick up genetic traces of selection or adaptation in relation to dispersal by smaller-bodied frugivores, and (3) evaluate the macroevolution of candidate genes or gene families across the palm family. This project integrates the fields of plant evolution, molecular evolution and plant-frugivore interaction ecology. It will be in collaboration with researchers from Hohenheim University (Prof. Philipp Schlüter) and University of Miami (Prof. Mauro Galetti), among others.

Tasks:

  • Collecting genetic samples from H. coriacea individuals and populations on Madagascar and mainland Africa, and measuring their functional traits (part of these samples have already been collected);
  • Collecting ecological information about the seed dispersal effectiveness (e.g., using camera traps) and demography of H. coriacea in the study areas;
  • Using novel genomic and transcriptomic techniques (e.g., RAD-seq, RNA-seq) to infer candidate genes for functional traits and evaluate traces of selection;
  • 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. molecular biology, genetics, phylogenetics, population genomics, ecology and evolution). 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/mainland Africa). Therefore, prior experience with tropical natural history, fieldwork and basic living conditions is advantageous. Furthermore, the successful candidate should have prior experience using molecular techniques, preferably with transcriptomics or bioinformatics, incl. the basics of scripting/programming for handling and statistically analysing large genetic/genomic datasets. 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.

 

 

Legume trait meeting in Leipzig

In the beginning of March 2020, just before COVID-19 took over Europe, we organised a Legume trait meeting at iDiv (Leipzig, Germany) which was also the PhD kick-off meeting for the PhD project of Francisco Velásquez Puentes. For his PhD, he will study the role of functional traits during biome transitions in Neotropical legumes, as well as diversification mechanisms in relation to drought adaptations and dispersal – from macro- as well microevolutionary (population genomic) points of view.

Our guests – all legume/trait/biome experts – travelled from the UK – University of Exeter (Toby Pennington), University of Edinburgh (Kyle Dexter, Flávia Pezzini)  – and Switzerland – University of Zurich (Colin Hughes, Erik Koenen, Jens Ringelberg, Elin Ruetimann). The 3 day meeting was insightful and initiated new ideas and initiatives which will hopefully substantialize in the coming years.

New article: Primate colour vision linked to palm fruit colours

Press release by iDiv (Kati Kietzmann)

Read the open access article here

Data for the article can be downloaded here

Colourful fruits may be the reason why primates can distinguish between shades of red, green and blue

Leipzig/Amsterdam. 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.

Original publication

Onstein RE, Vink DN, Veen J, Barratt CD, Flantua SGA, Wich SA, Kissling WD (2020). Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems. Proc. R. Soc. B 20192731. DOI: 10.1098/rspb.2019.2731

http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2019.2731

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

Screen Shot 2020-02-28 at 09.36.54

The fate of megafaunal plants on Madagascar: the video

Link to video: https://vimeo.com/390453594

Plants with megafaunal fruits on Madagascar used to rely on megafaunal animals, such as giant lemurs and elephant birds, for their dispersal. Nowadays, these animals are extinct, and this may lead to dispersal limitation of plants with megafaunal fruits, and possibly their extinction. This video uses animations and footage from Madagascar to present our research to understand the consequences of megafaunal extinctions for palms with megafaunal fruits, and whether they need conservation prioritisation.

This video was made in collaboration with TRICKLABOR for the amazing animations. I also obtained an Outreach grant from the European Society of Evolutionary Biology (ESEB) and a grant from iDiv’s Female Scientist Career Fund to make this film project happen.

In the coming years we hope to find answers to the questions proposed in the video

Jungle_B6 copy

Trait flexibility leading to angiosperm success

As part of the “Tansley Medal” competition of the journal New Phytologist, I was asked to write a short (max 2500 words) Tansley Insight article. I applied for the competition a year ago, and was informed last April that I was short-listed. This pushed me to finally write this review, of which the topic dates from my PhD times.

I did my PhD at the University of Zurich as part of the ‘Cenozoic Angiosperm Radiation’ (CAR) project led by Prof. Peter Linder (who recently retired). The CAR team included several people, among them Colin Hughes, Yaowu Xing, Yanis Bouchenak-Khelladi and Erik Koenen. We would have Tuesday afternoon beers for several years to discuss ideas and projects. The main aim was to understand angiosperm radiations from phylogenies, fossils and functional traits, and we managed to tackle this question in several angiosperm clades, such as Fagales, Rhamnaceae, Proteaceae and Ericaceae. The emergent patterns across clades showed that radiations, or evolutionary diversification, is often the result of the intricate interaction between traits and environments. Screen Shot 2019-12-19 at 11.52.01

What remained an unanswered question, to me at least, was why angiosperms seem to have managed to radiate much more than other plant clades, such as gymnosperms, and also why not all angiosperm clades do equally well (in terms of their diversification rate). This question is not new, it was already proposed by Darwin (his second ‘abominable mystery’) and reviewed by Crepet and Niklas in 2009.

What I propose in my review, is that angiosperms (compared with gymnosperms) and species-rich angiosperm lineages (compared with species-poor lineages) have had (1) many trait innovations, (2) many ecological opportunities that emerged during Cenozoic global changes and (3) ‘trait flexibility’ to explore the functional space of novel traits, allowing for rapid adaptation to novel environments. These three ‘ingredients’ combined could lead to increased diversification rates. I quantified the support for this idea by performing a systematic review across the literature for trait-dependent diversification rates (key innovations) and trait transition rates (trait flexibility). Indeed, it seems that although no trait consistently leads to radiation across angiosperms, certain lineages may be predisposed to evolve the right traits in the right place at the right time, suggesting trait flexibility. This may have a genetic basis, and may explain why angiosperms have risen to dominance in most terrestrial ecosystems during the Cenozoic (i.e., the last 66 million years).

Hopefully it’s good enough to win the Tansley Medal.

Reference:

Onstein, RE (in press). “Darwin’s second ‘abominable mystery’: trait flexibility as the innovation leading to angiosperm diversity” New Phytologist. [ABSTRACT].