Research Leader for the DarkTree Project

The Swedish Museum of Natural History is a government agency with a mandate to promote knowledge, research and interest in our world. It is a prominent research institution and Sweden's largest museum. For more than 200 years, the museum has been collecting specimens and data and conducting research on life on earth. The collections contain more than 11 million plants, animals, fungi, environmental samples, minerals and fossils. All research and knowledge are shared in the exhibitions, Cosmonova and in activities at the museum and digitally.

In the Department of bioinformatics and genetics, we are using information technology and genetic methods to study biological diversity and evolution. We are now looking for a research leader for the DarkTree project, funded by the Knut and Alice Wallenberg Foundation. The position will be placed in the research group led by professor Fredrik Ronquist (https://ronquistlab.github.io/ (https://ronquistlab.github.io/)), focused on data-driven research on insect diversity and evolution.

In this research project you will work within a highly collaborative, interdisciplinary team with the goal of filling in the current gaps in the insect tree of life using a combination of genome sequencing, computer vision and probabilistic machine learning. We will be using a unique insect material collected in the Insect Biome Atlas project (funded by the Knut and Alice Wallenberg Foundation) and LIFEPLAN project (funded by the European Research Council), comprising some 50,000 Malaise trap samples containing an estimated 50 million insects representing at least a million species, most of which are undescribed. All samples have been previously indexed using metabarcoding of the mitochondrial gene CO1, commonly used for species identification in insects.

WORK TASKS

Using the metabarcoding information and the current genome-based tree of life for insects, we will systematically pick out specimens of species-rich but poorly known groups for genome sequencing. The process will involve computer-assisted manual sorting of samples, individual-specimen barcoding to verify the species identification, and finally genome sequencing and phylogenetic inference aimed at providing a backbone within the darkest regions in the current genome-based insect tree of life.

The resulting data will be used to study the diversification of insects through time, the evolution of insect genomes, and the co-evolution of insects and their symbionts. We will also target methods for improved noise reduction and taxonomic annotation of metabarcoding data. The project will involve methods development at the cutting edge of AI, computer vision and probabilistic machine learning. The project is a collaboration between researchers at the Swedish Museum of Natural History, KTH Royal Institute of Technology and Linköping University, and also involves an advisory group consisting of additional researchers from Sweden and abroad.

You will be responsible for setting up a high-throughput pipeline for genome assembly and generation of suitable datasets for phylogenomic analysis. In collaboration with other project members, you will help develop the evolutionary models, error analysis techniques, and machine learning approaches that we will use in the phylogenomic analysis, the placement of the barcode sequences in this genomic backbone tree, and the processing of the raw metabarcoding data. An important challenge will be to scale up probabilistic machine learning techniques so that they can be applied to the large data sets we will be generating in the project. The aim is to generate 3,000 insect genomes targeting dark regions in the insect tree during the project period. We plan to combine this with up to 2,000 genomes generated by others in inferring the genomic backbone tree, which will then be decorated with at least 1 million barcode sequences from the Insect Biome Atlas and LIFEPLAN projects. The work will involve travel, organization of project meetings, and outreach activities.

QUALIFICATIONS

We are looking for a candidate with a PhD and postdoctoral research experience in phylogenomics. You should have a solid background in bioinformatics, statistical phylogenetics and comparative genomics. Previous experience of working with denovo assemblies and insects would be meritorious. The work requires excellent skills in written and oral communication in English. Skills in written and oral communication in Swedish would be meritorious.

We are looking for a candidate with strong analytical and communicative skills, and who is results-oriented.

OTHER

This is a temporary employment for a period of four years from the starting date.

We advance our knowledge of the natural world, inspiring to better care of our planet. Our ambition is that the employees of The Swedish Museum of Natural History shall represent the diversity in Sweden and we welcome every applicant.

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