A four-year full-time position as researcher in insect phylogenomics
is available in Stockholm. The successful candidate will be a joint
member of the Ronquist lab at the Swedish Museum of Natural History
(https://ronquistlab.github.io/) and the van der Valk lab at the Centre
for Palaeogenetics, Stockholm University / Swedish Museum of Natural
History (https://www.scilifelab.se/researchers/tom-van-der-valk/).

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
insect tree of life using the unique global insect material from the
Insect Biome Atlas (https://www.insectbiomeatlas.org/) and Lifeplan
(https://www.helsinki.fi/en/projects/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 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
platforms, 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.

Qualification requirements: We are looking for a candidate with a
PhD and postdoctoral research experience in phylogenomics. You should
have a strong background in bioinformatics, statistical phylogenetics
and comparative genomics. Previous experience of working with de novo
assemblies and insects would be meritorious.

About the employment: The employment is a temporary four-year
position. Scope of employment 100%. Starting date September 1, or
as agreed.

For further information about the position: please contact professor
Fredrik Ronquist, fredrik.ronquist@nrm.se, or Dr Tom van der Valk,
tom.vandervalk@nrm.se.

Application deadline: May 16, 2025.

For more information and to apply, please visit:
https://recruit.visma.com/spa/public/apply?guidAssignment=12b46c01-9af4-4ec4-b181-9dc224be598c&description=True

Fredrik Ronquist <Fredrik.Ronquist@nrm.se>

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