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!

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.

See you at Evolution in Montpellier?!

From 19-22 August 2018 I will attend the Evolution conference in Montpellier, France. I will present a poster on “Fruit colour as a driver for the evolution of trichromatic primate diversity” in S-33 Ecological models of macroevolution. Please visit me and / or my poster during the ‘Cocktail Poster Session 5.30pm –7.30pm’ on Tuesday 21st, or any other time!

 

Screen Shot 2018-08-08 at 13.57.14.png

Sneak preview….

The mutualism between fruits and frugivores is prominent in tropical rainforests, but to what extent fruits have influenced the macroevolution and macroecology of frugivores and their functional traits remains underexplored. Here, we hypothesize that trichromatic colour vision (i.e. the ability to distinguish green and red) in frugivorous primates has evolved as an adaptation to detect conspicuously coloured (i.e. reddish) fruits against a background of green foliage. The readily detection of these fruits as critical resources may have provided trichromatic primates a competitive advantage over dichromatic primates that cannot distinguish reds from greens.

Screen Shot 2018-08-08 at 14.06.49.png

To test this hypothesis, we combined global distribution, phylogenetic and colour vision data for >400 primate species with fruit colour data for >1700 palm and >80 fig species. Palms (Arecaceae) and figs (Ficus) are considered keystone resources for frugivores in tropical rainforests worldwide. We used structural equation modelling to show that the regional proportion of food plant species with conspicuously coloured fruits positively affects the diversity of trichromatic primates, but only in Africa. We show that this effect intensifies towards the tropics, following a hump-shaped relationship with food plant species richness. This suggests that the most species-rich places (i.e. rainforests) provide sufficient alternative food sources for primates, decreasing their dependence on conspicuous fruits. Overall, our results indicate that the consumption of palm and fig fruits could have been a driver for the diversification of trichromatic colour vision in African primates, and that food availability is an important determinant of frugivore diversity more generally.

 

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….

Screen Shot 2018-06-07 at 10.12.09

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).