Researcher in insect phylogenomics

A four-year full-time position as researcher in insect phylogenomics is available in the Ronquist lab. We are looking for someone with a passionate interest in insect phylogeny and evolution, and with strong competence in de novo genome assembly and phylogenomic analysis. The successful candidate will be a key member of the DarkTree project, funded by the Knut and Alice Wallenberg Foundation. The project aims to fill the gaps in the genome-based insect tree of life using the unique global insect material from the Insect Biome Atlas and Lifeplan projects. The material consists of around 50,000 Malaise trap samples, containing some 50 million insects representing more than 1 million species, most of which are currently undescribed. The entire material has gone through DNA metabarcoding using mild lysis protocols, providing a detailed index to the taxonomic content of each sample.

In DarkTree, we will use this material to systematically target the species-rich insect radiations that are not covered properly (or at all) by previous and ongoing genome sequencing efforts. The aim is to generate the first reasonably unbiased view of the insect tree of life, based on a backbone of some 5,000 genomes ‘decorated’ with at least 1 million DNA barcodes. The project involves collaboration with a computer vision lab at Linköping University, focused on developing AI-assisted techniques for picking out specimens for genome sequencing, and with computer scientists at KTH in Stockholm, focused on developing scalable probabilistic machine learning techniques for online phylogenomic analysis and placement of DNA barcodes.

You will be responsible for setting up a high-throughput pipeline for de novo assembly of genomes from short-read Illumina sequencing, and processing of the assemblies to generate suitable datasets for phylogenomic analysis. Together with other team members, you will also be developing and implementing the evolutionary models used in the phylogenomic analyses, and in interpreting and publishing the results. There will be considerable freedom in developing your own research projects based on the data we generate in the project.

Read more about the position and apply here. Application deadline May 16, 2025.